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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Parametric dynamic mode decomposition for reduced order modeling

Dynamic Mode Decomposition (DMD) is a model-order reduction approach, whereby spatial modes of fixed temporal frequencies are extracted from numerical or experimental data sets. The DMD low-rank or reduced operator is typically obtained by singular value decomposition of the temporal data sets. For parameter-dependent models, as found in many multi-query applications such as uncertainty quantification or design optimization, the only parametric DMD technique developed was a stacked approach, with data sets at multiple parameter values were aggregated together, increasing the computational work needed to devise low-rank dynamical reduced-order models. Here in this paper, we present two novel approach to carry out parametric DMD: one based on the interpolation of the reduced-order DMD eigen-pair and the other based on the interpolation of the reduced DMD (Koopman) operator. Numerical results are presented for diffusion-dominated nonlinear dynamical problems, including a multiphysics radiative transfer example. All three parametric DMD approaches are compared.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

GeN-ROM—An OpenFOAM®-based multiphysics reduced-order modeling framework for the analysis of Molten Salt Reactors

This work presents a projection-based multiphysics Model Order Reduction (MOR) framework for the analysis of nuclear systems and its application to parametric simulations of Molten Salt Reactors (MSR). The framework, named GeN-ROM, is developed using OpenFOAM® and employs a Proper Orthogonal Decomposition aided Reduced-Basis technique (POD-RB). It can be used to reduce steady-state and transient multiphysics problems involving parametric fluid dynamics, heat exchange, and neutronics phenomena. For the treatment of structural elements in the hydraulic systems, a porous medium approach has been adopted. The reduction process is data-driven and snapshot information is extracted via POD to learn the solution manifold and to build global spatial basis functions. At the data collection phase, GeN-ROM makes use of the solvers available in GeN-Foam, a similarly OpenFOAM®-based multiphysics framework developed for the analysis of nuclear reactors. The global bases are used both to approximate the solution fields and to project the full-order equations onto lower-dimensional subspaces, thus considerably reducing the number of unknowns in a numerical system. This reduction leads to significant computational speedups, which is ideal for multi-query applications such as uncertainty quantification or design optimization. The developed tool has been tested using a 2D multiphysics model of the Molten Salt Fast Reactor (MSFR) with steady-state and transient scenarios, with speedups on the order of 10 – 10 5 .

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2018

Parallelized hybrid optimization methods for nonsmooth problems using NOMAD and linesearch

Two parallelized hybrid methods are presented for single-function optimization problems with side constraints. The optimization problems are difficult not only due to possible existence of local minima and nonsmoothness of functions, but also due to the fact that objective function and constraint values for a solution vector can only be obtained by querying a black box whose execution requires considerable computational effort. Examples are optimization problems in Engineering where objective function and constraint values are computed via complex simulation programs, and where local minima exist and smoothness of functions is not assured. The hybrid methods consist of the well-known method NOMAD and two new methods called DENCON and DENPAR that are based on the linesearch scheme CS-DFN. The hybrid methods compute for each query a set of solution vectors that are evaluated in parallel. The hybrid methods have been tested on a set of difficult optimization problems produced by a certain seeding scheme for multiobjective optimization. We compare computational results with solution by NOMAD, DENCON, and DENPAR as stand-alone methods. It turns out that among the stand-alone methods, NOMAD is significantly better than DENCON and DENPAR. However, the hybrid methods are definitely better than NOMAD.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Efficient Active Learning for Gaussian Process Classification by Error Reduction

Active learning sequentially selects the best instance for labeling by optimizing an acquisition function to enhance data/label efficiency. The selection can be either from a discrete instance set (pool-based scenario) or a continuous instance space (query synthesis scenario). In this work, we study both active learning scenarios for Gaussian Process Classification (GPC). The existing active learning strategies that maximize the Estimated Error Reduction (EER) aim at reducing the classification error after training with the new acquired instance in a onestep-look-ahead manner. The computation of EER-based acquisition functions is typically prohibitive as it requires retraining the GPC with every new query. Moreover, as the EER is not smooth, it can not be combined with gradient-based optimization techniques to efficiently explore the continuous instance space for query synthesis. To overcome these critical limitations, we develop computationally efficient algorithms for EER-based active learning with GPC. Further, we derive the joint predictive distribution of label pairs as a one-dimensional integral, as a result of which the computation of the acquisition function avoids retraining the GPC for each query, remarkably reducing the computational overhead. We also derive the gradient chain rule to efficiently calculate the gradient of the acquisition function, which leads to the first query synthesis active learning algorithm implementing EER-based strategies. Our experiments clearly demonstrate the computational efficiency of the proposed algorithms. We also benchmark our algorithms on both synthetic and real-world datasets, which show superior performance in terms of sampling efficiency compared to the existing state-of-the-art algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Optimized self-designing key-value storage engine

Embodiments of the invention utilize an optimized key-value storage engine to strike the optimal balance between cloud-cost and performance and supports queries, including updates, lookups, range queries, inserts, and read-modify-writes. Cloud cost is manifested in purchasing both storage and processing resources. The improved approach has the ability to self-design and instantiate holistic configurations given a workload, a cloud budget, and optionally performance goals and a set of Service Level Agreement (SLA) specifications. A configuration reflects an optimized storage engine design in terms of, for example, the individual data structures design (in-memory and on-disk) in the engine as well as their algorithms and interactions, a cloud provider, and the exact virtual machines to be used.

Idreos, Stratos↗
DOE OSTI2022

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↗
DOE OSTI2019

Exploration and Analysis of Legacy Data at the Hanford Site Using PHOENIX - 19044

Radioactive contaminants pose risks to human health and the environment. These risks are influenced by factors such as disposal/release and transport mechanisms, location in the environment, potential exposure receptors, and the presence of comingled contaminants. Understanding the behavior, transport, and distribution of radionuclides in the environment is essential to facilitating risk-informed decision-making related to remedial design, action, and monitoring. These decisions are based on significant amounts of complex data that must be accessed, integrated, and analyzed to effectively evaluate data and formulate appropriate conclusions and recommendations. Often, data volume, complexity, and legacy access issues pose severe challenges for analysts, regulators, and stakeholders interested in evaluating scientific data to support decision-making. To address these challenges at the U.S. Department of Energy Hanford Site, Pacific Northwest National Laboratory (PNNL) has developed PHOENIX (PNNL-Hanford Online Environmental Information exchange) to facilitate risk-informed decision-making by streamlining investigative and analytical processes through the integration and visualization of previously isolated datasets created under distinct regulatory or operational regimes, each serving a specific purpose. With the large volume of data dispersed across many Hanford environmental databases, finding the correct sources of relevant data, accessing them, and relating them in a meaningful way can prove challenging and time consuming. By analyzing Hanford databases, performing substantial optimization using modern data processing methods and developing extensive queries on the refactored data, PHOENIX enables users to access, integrate, display, visualize, and retrieve data that would have been historically unfeasible to examine. The data and information accessible through PHOENIX help inform remediation-related assessments and evaluations, predict and quantify the risks that radioactive and chemical contaminants pose to human health and the environment, and communicate this information to decision makers responsible for risk-based remediation actions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Robust Multi-fidelity Bayesian Optimization with Deep Kernel and Partition

Multi-fidelity Bayesian optimization (MFBO) is a powerful approach that utilizes lowfidelity, cost-effective sources to expedite the exploration and exploitation of a high-fidelity objective function. Existing MFBO methods with theoretical foundations either lack justification for performance improvements over single-fidelity optimization or rely on strong assumptions about the relationships between fidelity sources to construct surrogate models and direct queries to low-fidelity sources. To mitigate the dependency on cross-fidelity assumptions while maintaining the advantages of low-fidelity queries, we introduce a random sampling and partition-based MFBO framework with deep kernel learning. This framework is robust to cross-fidelity model misspecification and explicitly illustrates the benefits of low-fidelity queries. Our results demonstrate that the proposed algorithm effectively manages complex cross-fidelity relationships and efficiently optimizes the target fidelity function.

Zhang, Fengxue [University of Chicago, Illinois, U↗
DOE OSTI2026

ECLEIRS: Exact conservation law embedded identification of reduced states for parameterized nonlinear conservation laws from sparse and noisy data

Multi-query applications such as parameter estimation, uncertainty quantification and design optimization for parameterized partial differential equation (PDE) systems are expensive. While reduced/latent state dynamics approaches for parameterized PDEs offer a viable alternative, these approaches rely on high-quality data and struggle with highly sparse spatiotemporal noisy measurements typically obtained from experiments. Furthermore, there is no guarantee that these models satisfy governing physical conservation laws. In this article, we propose a reduced state dynamics approach, referred to as ECLEIRS, that embeds exact conservation in the solution and flux representation by utilizing a space-time divergence-free neural network formulation. We compare ECLEIRS with other reduced state dynamics approaches, those that do not enforce any physical constraints and those with physics-informed loss functions, for three shock-propagation problems: 1-D advection, 1-D Burgers and 2-D Euler equations. In conclusion, the numerical experiments conducted in this study demonstrate that ECLEIRS provides the most accurate prediction of dynamics for unseen parameters even in the presence of highly sparse and noisy data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Towards a Heterogeneous, Polystore-like Data Architecture for the US Department of Veteran Affairs (VA) Enterprise Analytics

The Polystore architecture revisits the federated approach to access and querying of the standalone, independent databases in the uniform and optimized fashion, but this time in the context of heterogeneous data and specialized analyses. In the light of this architectural philosophy, and in the light of the major data architecture development efforts at the US Department of Veterans Administration (VA), we discuss the need for the heterogeneous data store consisting of the large relational data warehouse, an image and text datastore, and a peta-scale genomic repository. The VA's heterogeneous datastore would, to a larger or smaller degree, follow the architectural blueprint proposed by the polystore architecture. To this end, we discuss the current state of the data architecture at VA, architectural alternatives for development of the heterogeneous datastore, the anticipated challenges, and the drawbacks and benefits of adopting the polystore architecture.

Federated Databases↗
DOE OSTI2026

Translation-Invariant Quantum Algorithms for Ordered Search are Optimal

Ordered search is the task of finding an item in an ordered list using comparison queries. The best exact classical algorithm for this fundamental problem uses [log 2 n] queries for a list of length n. Quantum computers can achieve a constant-factor speedup, but the best possible coefficient of log 2 n for exact quantum algorithms is only known to lie between (ln2)/π ≈ 0.221 and 4/log 2 605 ≈ 0.4333. We consider a special class of translation-invariant algorithms with no workspace, introduced by Farhi, Goldstone, Gutmann, and Sipser, that has been used to find the best known upper bounds. First, we show that any bounded-error, k-query quantum algorithm for ordered search can be implemented by a k-query algorithm in this special class. Second, we use linear programming to show that the best exact 5-query quantum algorithm can search a list of length 7265, giving an ordered search algorithm that asymptotically uses 5 log 7265 n ≈ 0.390 log 2 n quantum queries.

Translation-invariant quantum algorithms↗
DOE OSTI2023

Evaluation of dual-weighted residual and machine learning error estimation for projection-based reduced-order models of steady partial differential equations

Projection-based reduced-order models (pROMs) show great promise as a means to accelerate many-query applications such as forward error propagation, solving inverse problems, and design optimization. In order to deploy pROMs in the context of high-consequence decision making, accurate error estimates are required to determine the region(s) of applicability in the parameter space. The following paper considers the dual-weighted residual (DWR) error estimate for pROMs and compares it to another promising pROM error estimate, machine learned error models (MLEM). Here, we show how DWR can be applied to ROMs and then evaluate DWR on two partial differential equations (PDEs): a two-dimensional linear convection–reaction–diffusion equation, and a three-dimensional static hyper-elastic beam. It is shown that DWR is able to estimate errors for pROMs extrapolating outside of their training set while MLEM is best suited for pROMs used to interpolate within the pROM training set.

42 ENGINEERING↗
DOE OSTI2024

High-Dimensional Bayesian Optimization via Semi-Supervised Learning with Optimized Unlabeled Data Sampling

We introduce a novel semi-supervised learning approach, named Teacher-Student Bayesian Optimization (TSBO ), integrating the teacher-student paradigm into BO to minimize expensive labeled data queries for the first time. TSBO incorporates a teacher model, an unlabeled data sampler, and a student model. The student is trained on unlabeled data locations generated by the sampler, with pseudo labels predicted by the teacher. The interplay between these three components implements a unique selective regularization to the teacher in the form of student feedback. This scheme enables the teacher to predict high-quality pseudo labels, enhancing the generalization of the GP surrogate model in the search space. To fully exploit TSBO , we propose two optimized unlabeled data samplers to construct effective student feedback that well aligns with the objective of Bayesian optimization. Furthermore, we quantify and leverage the uncertainty of the teacher-student model for the provision of reliable feedback to the teacher in the presence of risky pseudo-label predictions. TSBO demonstrates significantly improved sample-efficiency in several global optimization tasks under tight labeled data budgets. The implementation is available at https://github.com/reminiscenty/TSBO-Official.

Yin, Yuxuan↗
DOE OSTI2025

Efficient online quantum circuit learning with no upfront training

Optimization is a promising candidate for studying the utility of variational quantum algorithms (VQAs). However, evaluating cost functions using quantum hardware introduces runtime overheads that limit exploration. Surrogate-based methods can reduce calls to a quantum computer, yet existing approaches require hyperparameter pre-training and have been tested only on small problems. Here, we show that surrogate-based methods can enable successful optimization at scale, without pre-training, by using radial basis function interpolation (RBF) to construct an adaptive, hyperparameter-free surrogate. Using the surrogate as an acquisition function drives hardware queries to the vicinity of the true optima. For 16-qubit random 3-regular Max-Cut instances with the Quantum Approximate Optimization Algorithm (QAOA), our method outperforms state-of-the-art approaches, without considering their upfront training costs. Furthermore, we successfully optimize QAOA circuits for 127-qubit random Ising models on an IBM processor using 10 4 −10 5 measurements. Strong empirical performance demonstrates the promise of automated surrogate-based learning for large-scale VQA applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Nearly-frustration-free ground state preparation

Solving for quantum ground states is important for understanding the properties of quantum many-body systems, and quantum computers are potentially well-suited for solving for quantum ground states. Recent work [1] has presented a nearly optimal scheme that prepares ground states on a quantum computer for completely generic Hamiltonians, whose query complexity scales as δ − 1 , i.e. inversely with their normalized gap. Here we consider instead the ground state preparation problem restricted to a special subset of Hamiltonians, which includes those which we term "nearly-frustration-free": the class of Hamiltonians for which the ground state energy of their block-encoded and hence normalized Hamiltonian α − 1 H is within δ y of -1, where δ is the spectral gap of α − 1 H and 0 ≤ y ≤ 1 . For this subclass, we describe an algorithm whose dependence on the gap is asymptotically better, scaling as δ y / 2 − 1 , and show that this new dependence is optimal up to factors of log ⁡ δ . In addition, we give examples of physically motivated Hamiltonians which live in this subclass. Finally, we describe an extension of this method which allows the preparation of excited states both for generic Hamiltonians as well as, at a similar speedup as the ground state case, for those which are nearly frustration-free.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Using advanced data structures to enable responsive security monitoring

Write-optimized data structures (WODS), offer the potential to keep up with cyberstream event rates and give sub-second query response for key items like IP addresses. These data structures organize logs as the events are observed. To work in a real-world environment and not fill up the disk, WODS must efficiently expire older events. As the basis for our research into organizing security monitoring data, we implemented a tool, called Diventi, to index IP addresses in connection logs using RocksDB (a write-optimized LSM tree). In this work, we extended Diventi to automatically expire data as part of the data structures’ normal operations. We guarantee that Diventi always tracks the N most recent events and tracks no more than N + k events for a parameter k < N, while ensuring the index is opportunistically pruned. To test Diventi at scale in a controlled environment, we used anonymized traces of IP communications collected at SuperComputing 2019. We synthetically extended the 2.4 billion connection events to 100 billion events. We tested Diventi vs. Elasticsearch, a common log indexing tool. In our test environment, Elasticsearch saw an ingestion rate of at best 37,000 events/s while Diventi sustained ingestion rates greater than 171,000 events/s. Our query response times were as much as 100 times faster, typically answering queries in under 80 ms. Furthermore, we saw no noticeable degradation in Diventi from expiration. We have deployed Diventi for many months where it has performed well and supported new security analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Ceramic Proppant Design for In-situ Microbially Enhanced Methane Recovery

This project designed a new type of multi-functional lightweight proppant. The proppant is utilized as the conventional lightweight proppant but also transports microorganisms to coalbed reservoirs. The proppant is coated with a polymer which protects the methanogenic microorganisms and serves as a time-release delivery for methane generation. To produce the multifunctional proppant, we assigned five tasks: 1) culturing methanogenic microbes from natural carbon sources; 2) identifying optimized growth and methanogenesis conditions for the microbial consortia; 3) synthesizing the lightweight ceramic proppant; 4) encapsulating the consortia and proppant; and 5) demonstrating lab scale simulated performance by monitoring in-situ methane generation and hydraulic conductivity. Task 1) To evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals, complex hydrocarbon sources, hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to 24 weeks were evaluated at 23°C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm for methane and 176,370 ppm for carbon dioxide. Task 2) A central composite design (CCD) was used to explore a broad range of operational conditions, examine the effects of the important environmental factors, such as temperature, pH and salt concentration, and query a feasible region of operation to maximize methane production from coal. Coal biogasification was optimal for this consortium at an initial pH value of 5.5, at 30 °C, and at a NaCl concentration 3.7 mg/cm 3 (i.e., 145,165 ppm). Task 3) To create the lightweight ceramic proppant, the kaolinite and iron oxide (Fe 2 O 3 ) mixture were sintered under reducing atmosphere varying partial pressures of oxygen from 1.7×10 -13 atm to 1.8×10-11 atm. The Fe 2 O 3 reduces to FeO and reacts with kaolinite decomposed to mullite to form Fe 2 SiO 4 , FeSiO 3 , and FeAl 2 O 4 . As a result the proppant develops large pores (~100 µm), giving it a low bulk density (1.43 g/cm 3 ), and high porosity (45.2 vol%) at P_(O_2 )of 1.8×10 -11 atm. The proppant sintered at P_(O_2 )of 1.7×10 -13 atm is characterized by smaller pores (26 µm), higher density (1.72 g/cm3) and lower porosity (37.5 vol%). Crush resistance testing at 9,000 psi yields 6.8 wt% fine particles increasing to 17.7 wt% in porous samples. Acid solubility varies from 5.5 wt% loss increasing to 12.9 wt% in porous samples. Task 4 and 5) The microbial consortia obtained from the optimized condition and lightweight proppant were encapsulated by calcium-alginate polymer. The encapsulation system, including microbes and a proppant, was stored at 20°C and 36°C. The sample stored at 36°C generated 7.1×[10] 3 ppm of methane at 670 h, whereas the sample incubated at 20°C generated 1.1×[10] 3 ppm of methane. Benchtop lab-scale bioreactors were constructed and showed with real-time measurements that, as the microbes produced methane, the pH decreased, and hydrogen and carbon dioxide gases were consumed. A calcium ion-selective sensor revealed the release mechanism of the microbes from encapsulation. The calcium ions interconnecting the alginate monomers were disassociated by counter cations such as protons and potassium ions. The counter cations bound to the carboxyl group on the alginate monomer, which thus lost its ionic interactions with the calcium ions, resulting in decomposition of the hydrogel structure. Furthermore, the conductivity was increased to ~700 mD-ft from ~530 mD-ft once the encapsulated sample was applied to the coal pack. The particle size of coal was reduced when the encapsulated sample was added to the coal. The reduced coal size implied that the microbes would consume the hydrocarbon in coal.

01 COAL, LIGNITE, AND PEAT↗