Search NASA⌕ Search

SEARCH · Search NASA

Results for “computational complexity”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5

Applying Quantum Computing to Simulate Power System Dynamics

Power system dynamics are generally modeled by high dimensional nonlinear differential-algebraic equations due to a large number of generators, loads, and transmission lines. Thus, its computational complexity grows exponentially with the system size. This paper demonstrates the potential use of quantum computing algorithms to model the power system dynamics. Leveraging a symbolic programming framework, we equivalently convert the power system dynamics’ differential algebraic equations (DAEs) into ordinary differential equations (ODEs), where the data of the state vector can be encoded into quantum computers via amplitude encoding. The system's nonlinearity is captured by Taylor polynomial expansion, the quantum state tensor, and Hamiltonian simulation, whereas state variables can be updated by a quantum linear equation solver. Our results show that quantum computing can simulate the dynamics of the power system with high accuracy, whereas its complexity is polynomial in the logarithm of the system dimension. Our work also illustrates the use of scientific machine learning tools for implementing scientific computing concepts, e.g., Taylor expansion, DAEs/ODEs transform, and quantum computing solver, in the field of power engineering.

Tran, Huynh↗

Unveiling User Behavior on Summit Login Nodes as a User

We observe and analyze usage of the login nodes of the leadership class Summit supercomputer from the perspective of an ordinary user—not a system administrator—by periodically sampling user activities (job queues, running processes, etc.) for two full years (2020–2021). Our findings unveil key usage patterns that evidence misuse of the system, including gaming the policies, impairing I/O performance, and using login nodes as a sole computing resource. Our analysis highlights observed patterns for the execution of complex computations (workflows), which are key for processing large-scale applications.

Wilkinson, Sean↗

2019 Budget Request for the DOE Computational Science Graduate Fellowship (CSGF) Grant

The Department of Energy Computational Science Graduate Fellowship (DOE CSGF) is necessary to meet the continual challenging national workforce needs that arise as computational science and engineering problems continue to grow in scope and complexity. Computational science and engineering (CSE) is a multidisciplinary approach that uses scientific computing to solve practical problems methods and to supply technical tools across the scientific discovery spectrum. In particular, the DOE CSGF emphasizes high-performance computing (HPC) that enables CSE that advances science and engineering in directions important to the DOE and the economy in general. Over the past half-century, HPC has been an essential tool for DOE’s success. During this period, important missions, such as nuclear stockpile stewardship, have turned to HPC as an essential technology. Entire science disciplines, such as biology and cosmology, have been transformed through the augmentation of scientific observation via HPC. At government laboratories and in industry, DOE CSGF alumni are helping push traditional HPC boundaries while contributing to discoveries in high-energy physics, renewable energy, fusion-reactor design, additive manufacturing, nanomaterials for next-generation batteries and transistors, and turbine and advanced nuclear reactor modeling. In addition, HPC is used to address national health needs that will eventually point to cures both by helping cancer researchers manage and analyze huge troves of data, by simulating biological mechanisms, and by accelerating drug development — including continuing to rise to the challenge of pandemic-related research. A 2023 report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR office, “Can the United States Maintain Its Leadership in High-Performance Computing?” says of the Program, “The CSGF program provides a barometer for disciplines that will be of interest to future DOE computing.” An explosion in scientific and technological data has driven the need for increasingly sophisticated HPC to transform those data into scientific understanding. With access to more and more data and the proliferation of HPC, Machine Learning and Artificial Intelligence are experiencing a renaissance, complementing the now well-established use of computational simulation. Indeed, in its September 2020 subcommittee report on “AI/ML, Data Intensive Science and High-Performance Computing”, the DOE Advanced Scientific Computing Advisory Committee (ASCAC) explicitly called for a fellowship program to train computational and data scientists to tackle exascale and data-intensive computing challenges. This collaboration of empirical and theory-based modeling will increasingly inform federal policymakers whose decisions affect American society and future generations, and it requires highly skilled and intellectually agile computational scientists who can support the fast-moving DOE National Laboratory research environment. In fact, the DOE CSGF program has explicitly and consistently addressed this need.

97 MATHEMATICS AND COMPUTING↗

A review of computational tools for design and reconstruction of metabolic pathways

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Comprehensive Informative Metric for Analyzing HPC System Status Using the LogSCAN Platform

Log processing by Spark and Cassandra-based ANalytics (LogSCAN) is a newly developed analytical platform that provides flexible and scalable data gathering, transformation and computation. One major challenge is to effectively summarize the status of a complex computer system, such as the Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). Although there is plenty of operational and maintenance information collected and stored in real time, which may yield insights about short- and long-term system status, it is difficult to present this information in a comprehensive form. In this work, we present system information entropy (SIE), a newly developed metric that leverages the powers of traditional machine learning techniques and information theory. By compressing the multivariant multi-dimensional event information recorded during the operation of the targeted system into a single time series of SIE, we demonstrate that the historical system status can be sensitively represented concisely and comprehensively. Given a sharp indicator as SIE, we argue that follow-up analytics based on SIE will reveal in-depth knowledge about system status using other sophisticated approaches, such as pattern recognition in the temporal domain or causality analysis incorporating extra independent metrics of the system.

Hui, Yawei↗

Defining quantum-ready primitives for hybrid HPC-QC supercomputing: a case study in Hamiltonian simulation

As computational demands in scientific applications continue to rise, hybrid high-performance computing (HPC) systems integrating classical and quantum computers (HPC-QC) are emerging as a promising approach to tackling complex computational challenges. One critical area of application is Hamiltonian simulation, a fundamental task in quantum physics and other large-scale scientific domains. This paper investigates strategies for quantum-classical integration to enhance Hamiltonian simulation within hybrid supercomputing environments. By analyzing computational primitives in HPC allocations dedicated to these tasks, we identify key components in Hamiltonian simulation workflows that stand to benefit from quantum acceleration. To this end, we systematically break down the Hamiltonian simulation process into discrete computational phases, highlighting specific primitives that could be effectively offloaded to quantum processors for improved efficiency. Our empirical findings provide insights into system integration, potential offloading techniques, and the challenges of achieving seamless quantum-classical interoperability. We assess the feasibility of quantum-ready primitives within HPC workflows and discuss key barriers such as synchronization, data transfer latency, and algorithmic adaptability. These results contribute to the ongoing development of optimized hybrid solutions, advancing the role of quantum-enhanced computing in scientific research.

97 MATHEMATICS AND COMPUTING↗

Ensemble Simulations on Leadership Computing Systems

Scientific productivity can be enhanced through workflow management tools, relieving large High Performance Computing (HPC) system users from the tedious tasks of scheduling and designing the complex computational execution of scientific applications. This paper presents a study on the usage of ensemble workflow tools to accelerate science using the Summit and Frontier supercomputing systems. The research aims to connect science domain simulations using Oak Ridge Leadership Computing Facility (OLCF) supercomputing platforms with ensemble workflow methods in order to accelerate HPC-enabled discovery and boost scientific impact. We present the coupling, porting and optimization of Radical-Cybertools on three applications: Chroma, NAMD and LAMMPS. The tools augment traditional HPC monolithic runs with a pilot scheduler. Lessons-learned are discussed for physics, biology and materials science applications. We discuss intrinsic limitations of coupling and porting ensemble workflow tools to applications that run on large HPC systems. The origins of technical challenges and their solutions developed during the implementation process are discussed. Data management strategies, OLCF’s policies for ensembles, and natively supported workflow tools are also summarized.

Georgiadou, Antigoni [ORNL] (ORCID:000000020977631↗

TChem v2.0 - A Software Toolkit for the Analysis of Complex Kinetic Models

TChem is an open source software library for solving complex computational chemistry problems and analyzing detailed chemical kinetic models. The software provides support for: complex kinetic models for gas-phase and surface chemistry; thermodynamic properties based on NASA polynomials; species production/consumption rates; stable time integrator for solving stiff time ordinary differential equations; and, reactor models such as homogenous gas-phase ignition (with analytical Jacobian matrices), continuously stirred tank reactor, plug-flow reactor. This toolkit builds upon earlier versions that were written in C and featured tools for gas-phase chemistry only. The current version of the software was completely refactored in C++, uses an object-oriented programming model, and adopts Kokkos as its portability layer to make it ready for the next generation computing architectures i.e., multi/many core computing platforms with GPU accelerators. We have expanded the range of kinetic models to include surface chemistry and have added examples pertaining to Continuously Stirred Tank Reactors (CSTR) and Plug Flow Reactor (PFR) models to complement the homogenous ignition examples present in the earlier versions. To exploit the massive parallelism available from modern computing platforms, the current software interface is designed to evaluate samples in parallel, which enables large scale parametric studies, e.g. for sensitivity analysis and model calibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Paradeisos: A perfect hashing algorithm for many-body eigenvalue problems

Here, we describe an essentially perfect hashing algorithm for calculating the position of an element in an ordered list, appropriate for the construction and manipulation of many-body Hamiltonian, sparse matrices. Each element of the list corresponds to an integer value whose binary representation reflects the occupation of single-particle basis states for each element in the many-body Hilbert space. The algorithm replaces conventional methods, such as binary search, for locating the elements of the ordered list, eliminating the need to store the integer representation for each element, without increasing the computational complexity. Combined with the “checkerboard” decomposition of the Hamiltonian matrix for distribution over parallel computing environments, this leads to a substantial savings in aggregate memory. While the algorithm can be applied broadly to many-body, correlated problems, we demonstrate its utility in reducing total memory consumption for a series of fermionic single-band Hubbard model calculations on small clusters with progressively larger Hilbert space dimension.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference

Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

First principles calculations in support of Pu aging: calculating the effects of lattice imperfections on thermodynamics

Plutonium (Pu) has, in theory, well defined crystal structures: its atoms are arranged in regular spatial patterns. But Pu is radioactive, and as its nuclei decay those regular spatial patterns are interrupted. The interruptions are lattice imperfections, which are known to affect how materials respond to their environment. To adequately model Pu, we need to know which lattice imperfections are present, how they interact with each other, and how they affect the material’s response to its environment. The work presented here aims to use density functional theory (DFT) calculations to begin to answer the latter, in particular, how individual lattice imperfections affect measurable effects including thermal expansion (the change in volume in response to a change in temperature), heat capacity (the amount of thermal energy needed to change a material’s temperature), and elastic moduli (a material’s resistance to applied stresses). Pu poses many computational challenges. The $\textit{f}$ electrons require special attention. Of all the elements, Pu has the largest number of electrons that must be included in the calculations. Thermal effects require calculating the phonons (the lattice vibrations), which for systems containing lattice imperfections demand large, complex computational cells - but computational resources limit the size and complexity. With careful restructuring of how the calculations are performed, all these challenges have been met to enable calculations that provide insight into how lattice imperfections affect Pu’s response to its environment. Reported here are the computational challenges and the advances developed to meet them, along with the first results showing the strong effect that one prototype lattice imperfection (an interstitial Pu atom in a delta-phase Pu lattice) has on Pu’s response to its environment.

36 MATERIALS SCIENCE↗

Sensitivity and Uncertainty Workflow of Full System SIERRA Models Supporting High Consequence Applications

Credibility of end-to-end CompSim (Computational Simulation) models and their agile execution requires an expressive framework to describe, communicate and execute complex computational tool chains representing the model. All stakeholders from system engineering and customers through model developers and V&V partners need views and functionalities of the workflow representing the model in a manner that is natural to their discipline. In the milestone and in this report we define workflow as a network of computation simulation activities executed autonomously on a distributed set of computational platforms. The FY19 ASC L2 Milestone (6802) for the Integrated Workflow (IWF) project was designed to integrate and improve existing capabilities or develop new functionalities to provide a wide range of stakeholders a coherent and intuitive platform capable of defining and executing CompSim modeling from analysis workflow definition to complex ensemble calculations. The main goal of the milestone was to advance the integrated workflow capabilities to support the weapon system analysts with a production deployment in FY20. Ensemble calculations supporting program decisions include sensitivity analysis, optimization and uncertainty quantification. The goal of the L2 milestone aligned with the ultimate goal of the IWF project is to foster cultural and technical shift toward and integrated CompSim capability based on automated workflows. Specific deliverables were defined in five broad categories: 1) Infrastructure, including development of distributed-computing workflow capability, 2) integration of Dakota (Sandia's sensitivity, optimization and UQ engine) with SAW (Sandia Analysis Workbench), 3) ARG (Automatic Report Generator introspecting analysis artifacts and generating human-readable extensible and archivable reports), 4) Libraries and Repositories aiding capability reuse, and 5) Exemplars to support training, capturing best practices and stress testing of the platform. A set of exemplars was defined to represent typical weapon system qualification CompSim projects. Analyzing the required capabilities and using the findings to plan implementation of required capabilities ensured optimal allocation of development resources focused on production deployment after the L2 is completed. It was recognized early that the end-to-end modeling applications pose a considerable number of diverse risks, and a formal risk tracking process was implemented. The project leveraged products, capabilities and development tasks of IWF partners. SAW, Dakota, Cubit, Sierra, Slycat, and NGA (NexGen Analytics, a small business) contributed to the integrated platform developed during this milestone effort. New products delivered include: a) NGW (Next Generation Workflow) for robust workflow definition and execution, b) Dakota wizards, editor and results visualization, and c) the automatic report generator ARG. User engagement was initiated early in the development process eliciting concrete requirements and actionable feedback to assure that the integrated CompSim capability will have high user acceptance and impact. The current integrated capabilities have been demonstrated and are continually being tested by a set of exemplars ranging from training scenarios to computationally demanding uncertainty analyses. The integrated workflow platform has been deployed on both SRN (Sandia Restricted Network) and SCN (Sandia Classified Network). Computational platforms where the system has been demonstrated span from Windows (Creo the CAD platform chosen by Sandia) to Trinity HPC (Sierra and CTH solvers). Follow up work will focus on deployment at SNL and other sites in the nuclear enterprise (LLNL, KCNSC), training and consulting support to democratize the analysis agility, process health and knowledge management benefits the NGW platform provides.

97 MATHEMATICS AND COMPUTING↗

Kmer-SSR: a fast and exhaustive SSR search algorithm

Motivation: One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a ‘good enough’ solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a ‘good enough’ solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions. Results: We present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm. Availability and implementation: The source code is freely available on GitHub at https://github. com/ridgelab/Kmer-SSR.

59 BASIC BIOLOGICAL SCIENCES↗

ISAP-MATLAB Package for Sensitivity Analysis of High-Dimensional Stochastic Chemical Networks

Stochastic simulation and modeling play an important role to elucidate the fundamental mechanisms in complex biochemical networks. The parametric sensitivity analysis of reaction networks becomes a powerful mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, due to overwhelming computational cost, parametric sensitivity analysis is a extremely challenging problem for stochastic models with a high-dimensional parameter space and for which existing approaches are very slow. Here we present an information-theoretic sensitivity analysis in path-space (ISAP) MATLAB package that simulates stochastic processes with various algorithms and most importantly implements a gradient-free approach to quantify the parameter sensitivities of stochastic chemical reaction network dynamics using the pathwise Fisher information matrix (PFIM; Pantazis, Katsoulakis, and Vlachos 2013). The sparse, block-diagonal structure of the PFIM makes its computational complexity scale linearly with the number of model parameters. As a result of the gradientfree and the sparse nature of the PFIM, it is highly suitable for the sensitivity analysis of stochastic reaction networks with a very large number of model parameters, which are typical in the modeling and simulation of complex biochemical phenomena. Finally, the PFIM provides a fast sensitivity screening method (Arampatzis, Katsoulakis, and Pantazis 2015) which allows it to be combined with any existing sensitivity analysis software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Streaming Dynamic Mode Decomposition

We propose a reformulation of the streaming dynamic mode decomposition method that requires maintaining a single orthonormal basis, thereby reducing computational redundancy. The proposed efficient streaming dynamic mode decomposition method results in a constant-factor reduction in computational complexity and memory storage requirements. Numerical experiments on representative canonical dynamical systems show that the enhanced computational efficiency does not compromise the accuracy of the proposed method.

97 MATHEMATICS AND COMPUTING↗

Parallel Multivariate Spatio-Temporal Clustering of Large Ecological Datasets on Hybrid Supercomputers

A proliferation of data from vast networks of remote sensing platforms (satellites, unmanned aircraft systems (UAS), airborne etc.), observational facilities (meteorological, eddy covariance etc.), state-of-the-art sensors, and simulation models offer unprecedented opportunities for scientific discovery. Unsupervised classification is a widely applied data mining approach to derive insights from such data. However, classification of very large data sets is a complex computational problem that requires efficient numerical algorithms and implementations on high performance computing (HPC) platforms. Additionally, increasing power, space, cooling and efficiency requirements has led to the deployment of hybrid supercomputing platforms with complex architectures and memory hierarchies like the Titan system at Oak Ridge National Laboratory. The advent of such accelerated computing architectures offers new challenges and opportunities for big data analytics in general and specifically, large scale cluster analysis in our case. Although there is an existing body of work on parallel cluster analysis, those approaches do not fully meet the needs imposed by the nature and size of our large data sets. Moreover, they had scaling limitations and were mostly limited to traditional distributed memory computing platforms. We present a parallel Multivariate Spatio-Temporal Clustering (MSTC) technique based on k-means cluster analysis that can target hybrid supercomputers like Titan. We developed a hybrid MPI, CUDA and OpenACC implementation that can utilize both CPU and GPU resources on computational nodes. We describe performance results on Titan that demonstrate the scalability and efficacy of our approach in processing large ecological data sets.

Sreepathi, Sarat↗

Detecting anomalous behavior via user authentication graphs

Significant and aggregate user authentication activity may be analyzed across a population of users and computers in one or more networks to differentiate between authorized users and intruders in a network, and/or to detect inappropriate behavior by otherwise authorized users. Dynamic graphs and graph models over user and computer authentication activity, including time-constrained models, may be used for the purposes of profiling and analyzing user behavior in computer networks. More specifically, an edge-based breadth first search of graphs may be used that enforces time-constraints while maintaining traditional breadth first search computational complexity equivalence.

97 MATHEMATICS AND COMPUTING↗

How Many Trip Requests Could We Support? An Activity-Travel Based Vehicle Scheduling Approach

In a world of ever-changing travel behavior and ever-increasing modal options, is vital to have integrated models that could capture the interactions between supply and demand layers of travel. Addressing this need, we propose three different versions of network representation and mathematical models for the activity-based vehicle routing problem to connect activity-travel graphs of passengers (demand layer) to spatio-temporal networks of vehicles (supply layer). Versions I and II are arc-based, while version III is path-based. In version I, we introduce the concept of activity-travel graphs for passengers. For vehicles, we construct space–time networks and add a new dimension, called “under-service state”, to track the execution status of trip requests at any location and time. In version II, we reduce the complexity of the network structure by eliminating the state dimension and some other modifications in the structure of the passengers’ and vehicles’ network. Although both versions can capture various behavioral constraints of the activity-based vehicle routing problem (e.g., mandatory and optimal activities, duration of activities, chain of activities, preferred starting and ending times of activities), due to the high level of complexity of the network structure, both versions can only solve small-sized problems. To tackle the computational complexity, we propose a path-based network representation in version III, and to make a balance between the disutility of passengers and vehicles, we present a tolled user equilibrium problem. Mathematical models are coded in C and GAMS and implemented on real-world Phoenix regional transportation network with more than 39 million trip requests, which demonstrate the effectiveness of the proposed solution for the original and restricted master problems.

33 ADVANCED PROPULSION SYSTEMS↗