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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

PaKman: Scalable Assembly of Large Genomes on Distributed Memory Machines

De novo genome assembly is a fundamental problem in the field of bioinformatics, that aims to assemble the DNA sequence of an unknown genome from numerous short DNA fragments (aka reads) obtained from it. With the advent of high-throughput sequencing technologies, billions of reads can be generated in a matter of hours, necessitating efficient parallelization of the assembly process. While multiple parallel solutions have been proposed in the past, conducting a large- scale assembly at scale remains a challenging problem because of the inherent complexities associated with data movement, and irregular access footprints of memory and I/O operations. In this paper, we present a novel algorithm, called PaKman, to address the problem of performing large-scale genome assemblies on a distributed memory parallel computer. Our approach focuses on improving performance through a combination of novel data structures and algorithmic strategies for reducing the communication and I/O footprint during the assembly process. A key aspect of our algorithm is its graph data structure, which comprises fat nodes (or what we call "macro-nodes") that reduce the communication burden during contig generation. We present an extensive performance and qualitative evaluation of our algorithm, including comparisons to other state-of-the-art parallel assemblers. Our results demonstrate the ability to achieve near-linear speedups on up to 8K cores (tested); outperform state-of-the-art distributed memory and shared memory tools in performance while delivering comparable (if not better) quality; and reduce time to solution significantly. For instance, PaKman is able to complete an assembly of the full human genome in just over a minute on 8K cores.

Ghosh, Priyanka↗
DOE OSTI2014

Short ensembles: An Efficient Method for Discerning Climate-relevant Sensitivities in Atmospheric General Circulation Models

This paper explores the feasibility of an experimentation strategy for investigating sensitivities in fast components of atmospheric general circulation models. The basic idea is to replace the traditional serial-in-time long-term climate integrations by representative ensembles of shorter simulations. The key advantage of the proposed method lies in its efficiency: since fewer days of simulation are needed, the computational cost is less, and because individual realizations are independent and can be integrated simultaneously, the new dimension of parallelism can dramatically reduce the turnaround time in benchmark tests, sensitivities studies, and model tuning exercises. The strategy is not appropriate for exploring sensitivity of all model features, but it is very effective in many situations. Two examples are presented using the Community Atmosphere Model version 5. The first example demonstrates that the method is capable of characterizing the model cloud and precipitation sensitivity to time step length. A nudging technique is also applied to an additional set of simulations to help understand the contribution of physics-dynamics interaction to the detected time step sensitivity. In the second example, multiple empirical parameters related to cloud microphysics and aerosol lifecycle are perturbed simultaneously in order to explore which parameters have the largest impact on the simulated global mean top-of-atmosphere radiation balance. Results show that in both examples, short ensembles are able to correctly reproduce the main signals of model sensitivities revealed by traditional long-term climate simulations for fast processes in the climate system. The efficiency of the ensemble method makes it particularly useful for the development of high-resolution, costly and complex climate models.

atmospheric general circulation models↗
DOE OSTI2023

Up up down down left right left right B A Start for the catalytic hackers of programmable materials

Catalysts have advanced over the last century to accelerate and control reactions based on static active sites. More effective catalysis can be achieved using catalysts that change with time over the course of a reaction, providing a dynamic free energy landscape that is tailored to each step in the reaction sequence. Here, the catalyst is modulated via an input program that directs the surface to change physically or electronically with time, providing information regarding the extent and duration of change optimized for specific combinations of chemistry and programmable catalyst surfaces. While in its infancy, programmable catalysis is advancing with parallel efforts to establish fundamental principles of dynamic catalysts, design of programmable materials, and strategies to design input programs that will control catalysis for faster and more selective reactions.

catalyst↗
DOE OSTI2020

Intrinsic Ion Transport Properties of Block Copolymer Electrolytes

Knowledge of intrinsic properties is of central importance for materials design and assessing suitability for specific applications. Self-assembling block copolymer electrolytes (BCEs) are of great interest for applications in solid-state energy storage devices. A fundamental understanding of ion transport properties, however, is hindered by the difficulty in deconvoluting extrinsic factors, such as defects, from intrinsic factors, such as the presence of interfaces between the domains. Here, we quantify the intrinsic ion transport properties of a model BCE system consisting of poly(styrene-block-ethylene oxide) (SEO) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt using a generalizable strategy of depositing thin films on interdigitated electrodes and self-assembling fully connected parallel lamellar structures throughout the films. Comparison between conductivity in homopolymer poly(ethylene oxide) (PEO)-LiTFSI electrolytes and the analogous conducting material in SEO over a range of salt concentrations (r, molar ratio of lithium ion to ethylene oxide repeat units) and temperatures reveals that between 20% and 50% of the PEO in SEO is inactive. Using mean-field theory calculations of the domain structure and monomer concentration profiles at domain interfaces-both of which vary substantially with salt concentration-the fraction of inactive PEO in the SEO, as derived from conductivity measurements, can be quantitatively reconciled with the fraction of PEO that is mixed with greater than a few volume percent of polystyrene. Despite the detrimental interfacial effects for ion transport in BCEs, the intrinsic conductivity of the SEO studied here (ca. 10 -3 S/cm at 90 degrees C, r = 0.085) is an order of magnitude higher than reported values from bulk samples of similar molecular weight SEO (ca. 10 -4 S/cm at 90 degrees C, r = 0.085). Finally, this work provides motivation and methods for pursuing improved BCE chemical design, interfacial engineering, and processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Model-based, in-situ, non-destructive qualification and certification of parts made by autonomous additive manufacturing

To address the significant productivity challenges associated with the qualification and certification (Q&C) tasks of additively manufactured (AM) parts, which have traditionally relied on rigorous post‐build inspection and testing, we propose an integrated framework that combines model‐based qualification and certification (MBQ&C) with autonomous additive manufacturing (AAM). MBQ&C employs high‐fidelity predictive models, developed within the Integrated Computational Materials Engineering (ICME) paradigm, to simulate process–structure–property–performance relationships for assessing a part’s fitness for use. Since predictive models are commonly machine learning (ML)-based or reduced-order surrogates of validated physics models, they run efficiently, enabling timely inference. In parallel, the self-driving AAM utilises ML-based adaptive, closed‐loop control strategies to avoid, mitigate, or repair defects and anomalies during fabrication, thereby increasing the likelihood of producing acceptable parts. A key feature of the combined AAM-MBQ&C framework is that predictive models explicitly incorporate defects or anomalies that persist after the build, using instance-specific data captured via in-situ sensing. This customisation enables a build‐specific assessment of fitness for use, rather than relying on nominal or generic parameters. Such individualised evaluation provides a robust basis for Q&C-related acceptance decisions relating to each build. Additionally, the rapid solution capabilities of ML or reduced-order models enable the determination of a part’s suitability for service shortly after build completion. As the framework matures, it has the potential to substantially reduce reliance on conventional point‐design approaches—such as time‐consuming post‐build computed tomography scanning and costly destructive testing. Thus, the AAM-MBQ&C framework represents a transformative, scalable strategy for quality assurance of AM components, as parts produced within a stable, validated, and certified envelope can be certified with reduced testing. Key benefits include: (1) significant gains in Q&C productivity through efficient, model-centric assessment; (2) performance-based classification of defects into critical and non-critical categories; (3) the ability to predict potential deviations in the performance of parts affected by real-time, adaptive process control interventions relative to those produced under a certified process, and (4) the enabling of virtual Q&C for service environments that are difficult, hazardous, or impractical to access or reproduce experimentally. Collectively, these capabilities strengthen the business case for AM, particularly for high‐consequence and mission‐critical applications. Finally, although this work focuses on powder-based AM, the proposed techniques could be extended to AM processes employing alternative feedstock forms.

Gunasegaram, Dayalan↗
DOE OSTI2026

A Faster-Than-Real-Time Framework for Reliability-Oriented Simulation of PV Inverters

Physics-of-Failure (PoF) based reliability assessment for photovoltaic (PV) inverters requires long-duration electrical and electrothermal stress histories, yet generating such stress histories with high-fidelity switching models over year long mission profiles is computationally prohibitive. Conventional methods either sacrifice modeling fidelity for speed or require runtimes that are impractical for design iteration and uncertainty studies. To address this bottleneck, this paper presents a High-Performance Computing (HPC) based simulation frame work for faster-than-real-time reliability-oriented simulation. The proposed framework integrates the Average-to-Switching (A2S) method with parallel computing techniques to accelerate switching-level waveform reconstruction. We further introduce optimization strategies, including cluster merging and sensitivity based mission profile screening, to reduce the computational burden. Evaluated using real-world mission profile inputs and a MATLAB/Simulink switching-model reference, the framework reduces the simulation time for a one-year mission from an intractable multi-year duration to approximately 7.3 minutes while maintaining low waveform error. This acceleration provides a practical reliability-oriented simulation engine that can be coupled with component-specific aging models for subsequent PV inverter PoF assessment.

High-performance Computing↗
DOE OSTI2026

Relating Oxidative Protein Damage to Antioxidant Status in Health and Disease (Full Technical Report for 24-LW-026)

This two-year project evaluated how dietary antioxidants influence oxidative damage in cancer using complementary analytical and in-vivo approaches. We initially developed a protein oxidation labeling workflow and a parallel accelerator and molecular mass spectrometry (PAMMS) quantification method, but ultimately discontinued the labeling strategy due to unresolved separation challenges; PAMMS was instead leveraged to quantify radiolabeled catechol in rat plasma as a methodological benchmark. The biological study used a genetically engineered murine model (GEMM) for breast cancer (n = 40; four groups of 10: cancer/high antioxidant diet, cancer/normal diet, healthy/high-antioxidant diet, healthy/normal diet). In lieu of the abandoned labeling assay, untargeted metabolomics profiled plasma across groups, revealing widespread treatment-dependent changes in metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

A Case for Optimistic Coordination in HPC Storage Systems

High-performance computing (HPC) storage systems rely on access coordination to ensure that concurrent updates do not produce incoherent results. HPC storage systems typically employ pessimistic distributed locking to provide this functionality in cases where applications cannot perform their own coordination. This approach, however, introduces significant performance overhead and complicates fault handling. In this work we evaluate the viability of optimistic conditional storage operations as an alternative to distributed locking in HPC storage systems. We investigate design strategies and compare the two approaches in a prototype object storage system using a parallel read/modify/write benchmark. Our prototype illustrates that conditional operations can be easily integrated into distributed object storage systems and can outperform standard coordination primitives for simple update workloads. Our experiments show that conditional updates can achieve over two orders of magnitude higher performance than pessimistic locking for some parallel read/modify/write workloads.

Carns, Philip↗
DOE OSTI2025

Optimal Control Strategy With Efficiency and Reliability Improvement for Offshore DC Microgrids

Offshore microgrids, due to their remote location and lack of external energy support, face significant challenges in wide-range load operation and maintenance. Consequently, efficiency and reliability are critical concerns for converters in offshore dc microgrids. This article presents an optimal control strategy aimed at enhancing both efficiency and reliability. A normalized nonlinear relationship between power loss and thermal stress of a paralleled converter is first established. Based on this, a dual-objective optimization function with an active weight function as well as a system overall performance index is established. The active weight function dynamically adjusts the control priority based on converter efficiency and switching device thermal stress. Then, the optimal power-sharing strategy is derived by the Lagrange multiplier method with the proposed optimal function. Additionally, to accommodate a wide load range, an optimal selection strategy for operating converter combinations is proposed, requiring only low-bandwidth communication. Experiment verification is given to validate the effectiveness of the proposed control strategy. The experiment results demonstrate that the proposed control strategy can improve the overall performance of offshore microgrids by optimizing efficiency and reliability.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2019

Mobility Data and Models Informing Smart Cities

Using emerging data platforms, new mobility technologies, and travel demand models (TDMs), researchers, industry, and communities seek to improve the quality of transportation while maximizing the energy efficiency, equity, and safety of transportation services. As transportation may soon reach over 30% of U.S. energy consumption and with urban areas representing an increasing proportion of the U.S. population (>80% since 2010), a critical need exists to engage in urban data science-informed approaches to enhancing mobility. The objective of this study is to explore and document how aspiring Smart Cities are using data and models to inform mobility and energy initiatives within Smart City programs and in so doing identify gaps in knowledge and processes guiding Smart City mobility investment strategies, programs, projects, and pilots. A primary focus of the Smart Cities studied was the creation of an integrated data sharing environment approach. Most of these systems are being developed in parallel with multiple new data analysis tools, while regional metropolitan planning organizations continue to slowly evolve TDMs to take into account impacts of long-term strategies for emerging mobility technologies and services. Smart City initiatives in the United States have keen interests in leveraging knowledge and research on the mobility benefits and risks of automated, connected, efficient/electric, and shared on-demand mobility services; and understanding the related energy, environmental, economic, and societal impacts of these shifts. The results serve to identify key gaps in data, knowledge, and methods required to advance energy efficient urban mobility innovation, and to enable research and analysis collaboration between Smart Cities and the U.S. Department of Energy's efforts enabling new Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Porting hypre to heterogeneous computer architectures: Strategies and experiences

We report that linear systems are occurring in many applications, and solving them can take a large amount of the total simulation time. The high performance library hypre provides a variety of interfaces and linear solvers, including various multigrid methods, that have achieved good scalability on a variety of homogeneous parallel computer architectures. Heterogeneous architectures with nodes that have both CPUs and accelerators provide new challenges, since they require more fine-grained parallelism and reduced data movement between different memories on a single node as well as across nodes. We will discuss our experiences and strategies to port hypre to heterogeneous computers with accelerators, including the design of a new memory model, the use of abstractions, the BoxLoop macros in the structured and semi-structured interfaces, and the restructuring of algebraic multigrid (AMG) into modular components. We present numerical experiments comparing CPU and GPU performance for several test problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Best Practices and Lessons Learned from Deploying and Operating Large-Scale Data-Centric Parallel File Systems, In: SC '14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

The Oak Ridge Leadership Computing Facility (OLCF) has deployed multiple large-scale parallel file systems (PFS) to support its operations. During this process, OLCF acquired significant expertise in large-scale storage system design, file system software development, technology evaluation, benchmarking, procurement, deployment, and operational practices. Based on the lessons learned from each new PFS deployment, OLCF improved its operating procedures, and strategies. This paper provides an account of our experience and lessons learned in acquiring, deploying, and operating large-scale parallel file systems. We believe that these lessons will be useful to the wider HPC community.

Computer Science↗
DOE OSTI2013

Hydrocode Development on the Ncube and the Connection Machine Hypercubes [Book Chapter]

Hydrocode simulations constitute an important tool at Sandia National Laboratories and elsewhere for analyzing complex two- and three-dimensional systems. However, current vector supercomputers do not provide a growth path to enable fast, routine, and cost-effective simulations of large problems. Future, massively-parallel computers will provide a solution. Sandia has already developed simplified versions of the production hydrocode CTH for the Connection Machine and the nCUBE massively-parallel supercomputers. The parallel versions solve problems in two-dimensional, multi-fluid, shock-wave physics. Code development strategy, coding methodology, visualization techniques and performance results for this work are described.

640410 -- Fluid Physics-- General Fluid Dynamics↗
DOE OSTI2024

Optimizing Distributed Training on Frontier for Large Language Models

Large language models (LLMs) have demonstrated remarkable success as foundational models, benefiting various downstream applications through fine-tuning. Loss scaling studies have demonstrated the superior performance of larger LLMs compared to their smaller counterparts. Nevertheless, training LLMs with billions of parameters poses significant challenges and requires considerable computational resources. For example, training a one trillion parameter GPT-style model on 20 trillion tokens requires a staggering 120 million exaflops. This research explores efficient distributed training strategies to extract this computation from Frontier, the world's first exascale supercomputer. We enable and investigate various model and data parallel training techniques, such as tensor parallelism, pipeline parallelism, and sharded data parallelism, to facilitate training a trillion-parameter model on Frontier. We empirically assess these techniques and their associated parameters to determine their impact on memory footprint, communication latency, and GPU's computational efficiency. We analyze the complex interplay among these techniques and find a strategy to combine them to achieve high throughput through hyperparameter tuning. We have identified efficient strategies for training large LLMs of varying sizes through empirical analysis and hyperparameter tuning. For 22 Billion, 175 Billion, and 1 Trillion parameters, we achieved GPU throughputs of 38.38%, 36.14%, and 31.96%, respectively. For the training of the 175 Billion parameter model and the 1 Trillion parameter model, we achieved 100% weak scaling efficiency on 1024 and 3072 Mi250X GPUs, respectively. We also achieved strong scaling efficiencies of 89% and 87% for these two models. We trained these models only tens of iterations instead of training till completion.

Yin, Junqi↗
DOE OSTI2019

A Parallelised ROOT for Future HEP Data Processing

In the coming years, HEP data processing will need to exploit parallelism on present and future hardware resources to sustain the bandwidth requirements. As one of the cornerstones of the HEP software ecosystem, ROOT embraced an ambitious parallelisation plan which delivered compelling results. In this contribution the strategy is characterised as well as its evolution in the medium term. The units of the ROOT framework are discussed where task and data parallelism have been introduced, with runtime and scaling measurements. We will give an overview of concurrent operations in ROOT, for instance in the areas of I/O (reading and writing of data), fitting / minimization, and data analysis. This paper introduces the programming model and use cases for explicit and implicit parallelism, where the former is explicit in user code and the latter is implicitly managed by ROOT internally.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A survey on checkpointing strategies: Should we always checkpoint à la Young/Daly?

The Young/Daly formula provides an approximation of the optimal checkpointing period for a parallel application executing on a supercomputing platform. It was originally designed to handle fail-stop errors for preemptible tightly-coupled applications, but has been extended to other application and resilience frameworks. Here, we provide some background and survey various scenarios to assess the usefulness and limitations of the formula, both for preemptible applications and workflow applications represented as a graph of tasks. We also discuss scenarios with uncertainties, and extend the study to silent errors. We exhibit cases where the optimal period is of a different order than that dictated by the Young/Daly formula, and finally we explain how checkpointing can be further combined with replication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Scalable Implicit Solvers with Dynamic Mesh Adaptation for a Relativistic Drift-Kinetic Fokker–Planck–Boltzmann Model

In this work we consider a relativistic drift-kinetic model for runaway electrons along with a Fokker–Planck operator for small-angle Coulomb collisions, a radiation damping operator, and a secondary knock-on (Boltzmann) collision source. Here, we develop a new scalable fully implicit solver utilizing finite volume and conservative finite difference schemes and dynamic mesh adaptivity. A new data management framework in the PETSc library based on the p4est library is developed to enable simulations with dynamic adaptive mesh refinement (AMR), distributed memory parallelization, and dynamic load balancing of computational work. This framework and the runaway electron solver building on the framework are able to dynamically capture both bulk Maxwellian at the low-energy region and a runaway tail at the high-energy region. To effectively capture features via the AMR algorithm, a new AMR indicator prediction strategy is proposed that is performed alongside the implicit time evolution of the solution. This strategy is complemented by the introduction of computationally cheap feature-based AMR indicators that are analyzed theoretically. Numerical results quantify the advantages of the prediction strategy in better capturing features compared with nonpredictive strategies; and we demonstrate trade-offs regarding computational costs. The robustness with respect to model parameters, algorithmic scalability, and parallel scalability are demonstrated through several benchmark problems including manufactured solutions and solutions of different physics models. We focus on demonstrating the advantages of using implicit time stepping and AMR for runaway electron simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Priority-BF: A Task Manager for Priority-Based Scheduling

The increasing demand for computational resources, particularly in High-Performance Computing environments, necessitates to rethink how we handle job scheduling strategies. This work addresses the challenge of managing concurrent jobs with differing priorities on overloaded parallel systems, where strict QoS constraints are often difficult for users to define. Our solution relies on a qualitative description of priorities and pulls from two key approaches: the Easy-BF algorithm and the Conservative Backfilling algorithms. This solution improves the response time for high-priority jobs by 50% without affecting the overall system utilization. We show its applicability in several critical scenarios such as High-Performance Computing (HPC) resource management and in-situ computing.

Gainaru, Ana [ORNL]↗