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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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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Model-based Dynamic Control of Speculative Forays in Parallel Computation

In simulations running in parallel, the processors would have to synchronize with other processors to maintain correct global order of computations. This can be done either by blocking computation until correct order is guaranteed, or by \textit{speculatively} proceeding with the best guess (based on local information) and later correcting errors if/as necessary. Since the gainful lengths of speculative forays depend on the dynamics of the application software and hardware at runtime, an online control system is necessary to dynamically choose and/or switch between the blocking and speculative strategies. In this paper, we formulate the reversible speculative computing in large-scale parallel computing as a dynamic linear feedback control (optimization) system model and evaluate its performance in terms of time and cost savings as compared to the traditional (forward) computing. We illustrate with an exact analogy in the form of vehicular travel under dynamic, delayed route information. The objective is to assist in making the optimal decision on what computational approach is to be chosen, by predicting the amount of time and cost savings (or losing) under different environments represented by different parameters and probability distribution functions. We consider the cases of Gaussian, exponential and log-normal distribution functions. The control system is intended for incorporating into speculative parallel applications such as optimistic parallel discrete event simulations to decide at runtime when and to what extent speculative execution can be performed gainfully.

Perumalla, Kalyan↗
DOE OSTI2020

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Darshan for HEP applications

Modern HEP workflows must manage increasingly large and complex data collections. HPC facilities may be employed to help meet these workflows’ growing data processing needs. However, a better understanding of the I/O patterns and underlying bottlenecks of these workflows is necessary to meet the performance expectations of HPC systems.Darshan is a lightweight I/O characterization tool that captures concise views of HPC application I/O behavior. It intercepts application I/O calls at runtime, records file access statistics for each process, and generates log files detailing application I/O access patterns.Typical HEP workflows include event generation, detector simulation, event reconstruction, and subsequent analysis stages. A study of the I/O behavior of the ATLAS simulation and filtering stage, and the CMS simulation workflow using Darshan is presented, including insights into the I/O operations and data access size.

Wang, Rui↗
DOE OSTI2025

Lessons Learned and Scalability Achieved When Porting Uintah to DOE Exascale Systems

A key challenge faced when preparing codes for Department of Energy (DOE) exascale systems was designing scalable applications for systems featuring hardware and software not yet available at leadership-class scale. With such systems now available, it is important to evaluate scalability of the resulting software solutions on these target systems. One such code designed with the exascale DOE Aurora and DOE Frontier systems in mind is the Uintah Computational Framework, an open-source asynchronous many-task (AMT) runtime system. To prepare for exascale, Uintah adopted a portable MPI+X hybrid parallelism approach using the Kokkos performance portability library (i.e., MPI+Kokkos). This paper complements recent work with additional details and an evaluation of the resulting approach on Aurora and Frontier. Results are shown for a challenging benchmark demonstrating interoperability of 3 portable codes essential to Uintah-related combustion research. These results demonstrate single-source portability across Aurora and Frontier with scaling characteristics shown to 3,072 Aurora nodes and 9,216 Frontier nodes. In addition to showing results run to new scales on new systems, this paper also discusses lessons learned through efforts preparing Uintah for exascale systems.

Holmen, John [ORNL] (ORCID:0000000259342641)↗
DOE OSTI2015

Jagged Tiling for Intra-tile Parallelism and Fine-Grain Multithreading

In this paper, we have developed a novel methodology that takes into consideration multithreaded many-core designs to better utilize memory/processing resources and improve memory residence on tileable applications. It takes advantage of polyhedral analysis and transformation in the form of PLUTO, combined with a highly optimized finegrain tile runtime to exploit parallelism at all levels. The main contributions of this paper include the introduction of multi-hierarchical tiling techniques that increases intra tile parallelism; and a data-flow inspired runtime library that allows the expression of parallel tiles with an efficient synchronization registry. Our current implementation shows performance improvements on an Intel Xeon Phi board up to 32.25% against instances produced by state-of-the-art compiler frameworks for selected stencil applications.

compiler↗
DOE OSTI2025

Deployment of neural-network-based neutron microscopic cross sections in the Griffin reactor physics application

The capability to utilize neural networks to predict macroscopic and microscopic cross section parametric spaces has been developed for the Griffin reactor physics application. The LibTorch interface enables Griffin's MOOSE-based materials to interact with LibTorch-trained models, allowing for the evaluation of complex macroscopic or microscopic cross section spaces, which are then used to evaluate the neutronic properties of the Griffin finite element model. This study benchmarks traditional ISOXML-formatted tabulation libraries against neural network-based models for 279 nuclides on 20,160 grid points for zero-dimensional and two-dimensional reactor models. Benchmark metrics include the fundamental mode eigenvalue, fission and absorption rates, and various temperature coefficients of reactivity (isothermal, fuel, and moderator). From the perspective of storage space, the complete set of LibTorch models uses 11 MB on disk, compared to the 10 GB for the ISOXML multigroup library that covers the same grid space. For the two-dimensional performance case considered in Griffin, the Torch model uses 97% less RAM than the reference ISOXML dataset while runtime increases by a factor of 3 when using the LibTorch model compared to the ISOXML dataset with multi-linear interpolation. The LibTorch model consistently yields errors within 0.01% for most analyzed quantities except for the temperature coefficients of reactivity where the maximum discrepancies are up to 0.3 $\frac{pcm}{K}$. Due to the neural network attempting to best predict quantities with no regard for a positive or negative bias for any given quantity, predictions may experience random fluctuations, resulting in both positive and negative errors. Future work will entail both depletion and coupled transient analysis to determine the predictive capabilities of Griffin with neural network-based cross sections.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

GOTCHA

GOTCHA is a runtime API intercepting function calls between shared libraries. It is intended to be used by HPC Tools (i.e., performance analysis tools like Open/SpeedShop, HPCToolkit, TAU, etc.). 2:18 PMThese other tools can use Gotch to intercept interesting functions, such as MPI functions, and collect performance metrics about those functions. We intend for this to be open-source software that gets adopted by other open-s0urse tools that are used at LLNL.

Poliakoff, David↗
DOE OSTI2021

Performance evaluation of a Terry GS-2 steam impulse turbine with air-water mixtures

Terry steam turbines are widely used in various industries because of their robust design. Within the nuclear power generation industry, they are used in the Reactor Core Isolation Cooling System to remove decay heat during reactor isolation events. During the Fukushima Daiichi nuclear power station disaster in Japan in 2011, the Reactor Core Isolation Cooling System and associated Terry turbine operated for over 70 hours in Unit 2; this runtime is well beyond the expected operating duration. Theories suggest the turbine was subjected to a two-phase inlet flow, which could degrade the turbine performance. In this work, an experimental test rig was constructed to test a full-scale Terry model GS-2 steam turbine under two-phase air/water flows. Steady-state efficiency and torque performance maps of the turbine were developed over a range of turbine inlet pressures (1.38–4.83 bar or 20–70 psia), air mass fractions (0.05–1.0) and rotational speeds up to 4000 RPM. Furthermore, turbine performance followed expected trends with torque varying linearly and efficiency varying quadratically with rotational speed. In addition, high-speed images of the two-phase flow entering the turbine were also analyzed to understand how changes in inlet pressure and air mass fraction affect the flow regime and homogenization. The present tests with air–water two-phase mixtures are an important step towards providing an understanding of the full-scale Terry turbine’s behavior and performance curves under two-phase conditions. The results of this work will be combined with air/water and steam/water data gathered using a small-scale Terry ZS-1 steam turbine in order to understand the scaling relationship between large and small size Terry turbines and fluid pairs. The combined data set will enable further development of analytical models over a wide range of conditions and may be used to provide technical justification for expanded use of the Terry turbines in nuclear power plant safety systems and other systems.

42 ENGINEERING↗
DOE OSTI2022

Towards Low-Overhead Resilience for Data Parallel Deep Learning

Data parallel techniques have been widely adopted both in academia and industry as a tool to enable scalable training of deep learning models. At scale, DL training jobs can fail due to software or hardware bugs, may need to be preempted or terminated due to unexpected events, or may perform suboptimally because they were misconfigured. Under such circumstances, there is a need to recover and/or reconfigure data-parallel DL training jobs on-the-fly, while minimizing the impact on the accuracy of the DNN model and the runtime overhead. In this regard, state-of-art techniques adopted by the HPC community mostly rely on checkpoint-restart, which inevitably leads to loss of progress, thus increasing the runtime overhead. In this paper we explore alternative techniques that exploit the properties of modern deep learning frameworks (overlapping of gradient averaging and weight updates with local gradient computations through pipeline parallelism) to reduce the overhead of resilience/elasticity. To this end we introduce a failure simulation framework and two resilience strategies (immediate mini-batch rollback and lossy forward recovery), which we study compared with checkpoint-restart approaches in a variety of settings in order to understand the trade-offs between the accuracy loss of the DNN model and the runtime overhead.

data-parallel training↗
DOE OSTI2019

PAPI software-defined events for in-depth performance analysis

The methodology and standardization layer provided by the Performance Application Programming Interface (PAPI) has played a vital role in application profiling for almost two decades. It has enabled sophisticated performance analysis tool designers and performance-conscious scientists to gain insights into their applications by simply instrumenting their code using a handful of PAPI functions that “just work” across different hardware components. In the past, PAPI development had focused primarily on hardware-specific performance metrics. However, the rapidly increasing complexity of software infrastructure poses new measurement and analysis challenges for the developers of large-scale applications. In particular, acquiring information regarding the behavior of libraries and runtimes—used by scientific applications—requires low-level binary instrumentation, or APIs specific to each library and runtime. No uniform API for monitoring events that originate from inside the software stack has emerged. In this article, we present our efforts to extend PAPI’s role so that it becomes the de facto standard for exposing performance-critical events, which we refer to as software-defined events (SDEs), from different software layers. Upgrading PAPI with SDEs enables monitoring of both types of performance events—hardware- and software-related events—in a uniform way, through the same consistent PAPI. The goal of this article is threefold. First, we motivate the need for SDEs and describe our design decisions regarding the functionality we offer through PAPI’s new SDE interface. Second, we illustrate how SDEs can be utilized by different software packages, specifically, by showcasing their use in the numerical linear algebra library MAGMA-Sparse, the tensor algebra library TAMM that is part of the NWChem suite, and the compiler-based performance analysis tool Byfl. Third, we provide a performance analysis of the overhead that results from monitoring SDEs and discuss the trade-offs between overhead and functionality.

Jagode, Heike↗
DOE OSTI2018

LADR: low-cost application-level detector for reducing silent output corruptions

Applications running on future high performance computing (HPC) systems are more likely to experience transient faults due to technology scaling trends with respect to higher circuit density, smaller transistor size and near-threshold voltage (NTV) operations. A transient fault could corrupt application state without warning, possibly leading to incorrect application output. Such errors are called silent data corruptions (SDCs). In this paper, we present LADR, a low-cost application-level SDC detector for scientific applications. LADR protects scientific applications from SDCs by watching for data anomalies in their state variables (those of scientific interest). It employs compile-time data-flow analysis to minimize the number of monitored variables, thereby reducing runtime and memory overheads while maintaining a high level of fault coverage with low false positive rates. We evaluated LADR with 4 scientific workloads and results show that LADR achieved < 80% fault coverage with only ∼ 3% runtime overheads and ∼ 1% memory overheads. As compared to prior state-of-the-art anomaly-based detection methods, SDC achieved comparable or improved fault coverage, but reduced runtime overheads by 21% ∼ 75%, and memory overheads by 35% ∼ 55% for the evaluated workloads. We believe that such an approach with low memory and runtime overheads coupled with attractive detection precision makes LADR a viable approach for assuring the correct output from large-scale high performance simulations.

Chen, Chao↗
DOE OSTI2017

Benefit Analysis of Energy Storage for Cordova Electric Cooperative

This report is a follow on to a previous study performed by Sandia National Labs and Alaska Center for Energy and Power which investigated the use of an energy storage system (ESS) providing spinning reserve within the Cordova Electric Cooperative (CEC) grid. The study provided the savings using the ESS as spinning reserve through reduced fossil fuel consumption and runtime on the diesel generators. In this report, the saving values are used from the previous study to determine the benefit-to-cost ratio for various ratings of ESS performing spinning reserve and quantifying other applications that are applicable to CEC.

25 ENERGY STORAGE↗
DOE OSTI2018

Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models

The conductor–like polarizable continuum model (C–PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in quantum chemistry. We have previously implemented C–PCM solvation for Hartree–Fock (HF) and density functional theory (DFT) on graphical processing units (GPUs), enabling the quantum mechanical treatment of large solvated biomolecules. Here, we first propose a GPU–based algorithm for the PCM conjugate gradient linear solver that greatly improves the performance for very large molecules. The overhead for PCM–related evaluations now consumes less than 15% of the total runtime for DFT calculations on large molecules. Second, we demonstrate that our algorithms tailored for ground state C–PCM are transferable to excited state properties. Using a single GPU, our method evaluates the analytic gradient of the linear response PCM time–dependent density functional theory energy up to 80× faster than a conventional central processing unit (CPU)–based implementation. In addition, our C–PCM algorithms are transferable to other methods that require electrostatic potential (ESP) evaluations. For example, we achieve speed–ups of up to 130× for restricted ESP–based atomic charge evaluations, when compared to CPU–based codes. As a result, we also summarize and compare the different PCM cavity discretization schemes used in some popular quantum chemistry packages as a reference for both users and developers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

In-Situ Feature Extraction of Large Scale Combustion Simulations Using Segmented Merge Trees, In: SC '14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

The ever increasing amount of data generated by scientific simulations coupled with system I/O constraints are fueling a need for in-situ analysis techniques. Of particular interest are approaches that produce reduced data representations while maintaining the ability to redefine, extract, and study features in a post-process to obtain scientific insights. This paper presents two variants of in-situ feature extraction techniques using segmented merge trees, which encode a wide range of threshold based features. The first approach is a fast, low communication cost technique that generates an exact solution but has limited scalability. The second is a scalable, local approximation that nevertheless is guaranteed to correctly extract all features up to a predefined size. We demonstrate both variants using some of the largest combustion simulations available on leadership class supercomputers. Our approach allows state-of-the-art, feature-based analysis to be performed in-situ at significantly higher frequency than currently possible and with negligible impact on the overall simulation runtime.

Computer Science↗
DOE OSTI2020

Evaluating the Influence of Hemorheological Parameters on Circulating Tumor Cell Trajectory and Simulation Time

Extravasation of circulating tumor cells (CTCs) occurs primarily in the microvasculature, where flow and cell interactions significantly affect the blood rheology. Capturing cell trajectory at this scale requires the coupling of several interaction models, leading to increased computational cost that scales as more cells are added or the domain size is increased. In this work, we focus on micro-scale vessels and study the influence of certain hemorheological factors, including the presence of red blood cell aggregation, hematocrit level, microvessel size, and shear rate, on the trajectory of a circulating tumor cell. We determine which of the aforementioned factors significantly affect CTC motion and identify those which can potentially be disregarded, thus reducing simulation time. We measure the effect of these elements by studying the radial CTC movement and runtime at various combinations of these hemorheological parameters. To accurately capture blood flow dynamics and single cell movement, we perform high-fidelity hemodynamic simulations at a sub-micron resolution using our in-house fluid dynamics solver, HARVEY. We find that increasing hematocrit increases the likelihood of tumor cell margination, which is exacerbated by the presence of red blood cell aggregation. As microvessel diameter increases, there is no major CTC movement towards the wall; however, including aggregation causes the CTC to marginate quicker as the vessel size increases. Finally, as the shear rate is increased, the presence of aggregation has a diminished effect on tumor cell margination.

Roychowdhury, Sayan↗
DOE OSTI2019

Using Graph Partitioning for Scalable Distributed Quantum Molecular Dynamics

The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several advanced algorithms relying on evaluations of matrix polynomials have been published in the literature for such simulations. We aim to use a special type of graph partitioning to efficiently parallelize these computations. For this, we create a graph representing the zero–nonzero structure of a thresholded density matrix, and partition that graph into several components. Each separate submatrix (corresponding to each subgraph) is then substituted into the matrix polynomial, and the result for the full matrix polynomial is reassembled at the end from the individual polynomials. This paper starts by introducing a rigorous definition as well as a mathematical justification of this partitioning problem. We assess the performance of several methods to compute graph partitions with respect to both the quality of the partitioning and their runtime.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Application of linear prolongation to coarse mesh finite difference acceleration in CASMO5

The Coarse-Mesh Finite Difference (CMFD) method has been used for over a decade to accelerate the convergence of the Method of Characteristics (MOC) solution to the two- dimensional particle transport equation in CASMO5. Numerical testing, along with widespread use in production-level calculations, have shown that the current CMFD implementation provides stability and robustness for a wide range of realistic reactor physics problems. However, the recent development of linear prolongation has attracted attention from the community as a way to further improve the performance and stability of CMFD. Two interpolation methods for linear prolongation are presented in this work and implemented into a test version of CASMO5. The performance of the proposed interpolations, referred to as the bilinear and linear directional schemes, is evaluated in terms of runtime relative to the default constant or uniform scaling update. Numerical results indicate that the use of linear prolongation can reduce the transport solver runtime on average by approximately 10% when tested with two hundred randomly selected cases. The new directional linear interpolation, combined with default constant boundary updates, is found to provide the highest reduction in runtime for the cases analyzed. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

MatRIS: Addressing the Challenges for Portability and Heterogeneity Using Tasking for Matrix Decomposition (Cholesky)

The ubiquitous in-node heterogeneity of HPC and cloud computing platforms makes software portability and performance optimization extremely challenging. Described here, the MatRIS multilevel math library abstraction framework employs tasking to alleviate these difficulties. MatRIS includes the IRIS task-based runtime on the bottom level and exposes different layers of abstraction to render algorithms architecturally agnostic. MatRIS ensures the decomposition and creation of tasks that represent the necessary encapsulation of the optimized kernels from both vendor and open-source math libraries. Once built, MatRIS can select different combinations of accelerators at runtime, making it portable even on diverse heterogeneous architectures. By leveraging the IRIS runtime’s features for managing heterogeneity, MatRIS deploys algorithms that remove the need to specify orchestration and data transfer. This study describes how the serial task abstraction of a tiled Cholesky factorization is made portable and scalable in the case of multi-device and multi-vendor heterogeneity on a node with NVIDIA and AMD GPUs by using MatRIS. First, we demonstrate that Cholesky in MatRIS provides multi-GPU scalability that offers competitive performance versus cuSolverMG. Then, we present the challenges and opportunities for heterogeneous execution.

Monil, M. A. H.↗