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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Simulation of unsteady blood flows in a patient-specific compliant pulmonary artery with a highly parallel monolithically coupled fluid-structure interaction algorithm

Computational fluid dynamics (CFD) is increasingly used to study blood flows in patient-specific arteries for understanding certain cardiovascular diseases. The techniques work quite well for relatively simple problems, but need improvements when the problems become harder in the case when (1) the geometry becomes complex (from a few branches to a full pulmonary artery), (2) the model becomes more complex (from fluid-only calculation to coupled fluid-structure interaction calculation), (3) both the fluid and wall models become highly nonlinear, and (4) the computer on which we run the simulation is a supercomputer with tens of thousands of processor cores. To push the limit of CFD in all four fronts, in this paper, we develop and study a highly parallel algorithm for solving a monolithically coupled fluid-structure system for the modeling of the interaction of the blood flow and the arterial wall. As a case study, we consider a patient-specific, full size pulmonary artery obtained from CT (Computed Tomography) images, with an artificially added layer of wall with a fixed thickness. The fluid is modeled with a system of incompressible Navier-Stokes equations and the wall is modeled by a geometrically nonlinear elasticity equation. As far as we know this is the first time the unsteady blood flow in a full pulmonary artery is simulated without assuming a rigid wall. We report the proposed numerical algorithm and software scale well beyond 10,000 processor cores on a supercomputer for solving the fluid-structure interaction problem discretized with a stabilized finite element method in space and an implicit scheme in time involving hundreds of millions of unknowns.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Speeding up particle track reconstruction using a parallel Kalman filter algorithm

One of the most computationally difficult problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is determining the trajectory of charged particles during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material effects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filter-based methods for highly parallel, many-core SIMD architectures that are now prevalent in high-performance hardware. In this paper, we discuss the design and performance of the improved tracking algorithm, referred to as mkFit. A key piece of the algorithm is the Matriplex library, containing dedicated code to optimally vectorize operations on small matrices. The physics performance of the mkFit algorithm is comparable to the nominal CMS tracking algorithm when reconstructing tracks from simulated proton-proton collisions within the CMS detector. We study the scaling of the algorithm as a function of the parallel resources utilized and find large speedups both from vectorization and multi-threading. mkFit achieves a speedup of a factor of 6 compared to the nominal algorithm when run in a single-threaded application within the CMS software framework.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Reconstruction of Charged Particle Tracks in Realistic Detector Geometry Using a Vectorized and Parallelized Kalman Filter Algorithm

One of the most computationally challenging problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is finding and fitting particle tracks during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material e ects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filterbased methods for highly parallel, many-core SIMD and SIMT architectures that are now prevalent in high-performance hardware. Previously we observed significant parallel speedups, with physics performance comparable to CMS standard tracking, on Intel Xeon, Intel Xeon Phi, and (to a limited extent) NVIDIA GPUs. While early tests were based on artificial events occurring inside an idealized barrel detector, we showed subsequently that our mkFit software builds tracks successfully from complex simulated events (including detector pileup) occurring inside a geometrically accurate representation of the CMS-2017 tracker. Here, we report on advances in both the computational and physics performance of mkFit, as well as progress toward integration with CMS production software. Recently we have improved the overall eciency of the algorithm by preserving short track candidates at a relatively early stage rather than attempting to extend them over many layers. Moreover, mkFit formerly produced an excess of duplicate tracks; these are now explicitly removed in an additional processing step. We demonstrate that with these enhancements, mkFit becomes a suitable choice for the first iteration of CMS tracking, and eventually for later iterations as well. We plan to test this capability in the CMS High Level Trigger during Run 3 of the LHC, with an ultimate goal of using it in both the CMS HLT and oine reconstruction for the HL-LHC CMS tracker.

Cerati, Giuseppe↗
DOE OSTI2023

Exploring temporal community evolution: algorithmic approaches and parallel optimization for dynamic community detection

Abstract Dynamic (temporal) graphs are a convenient mathematical abstraction for many practical complex systems including social contacts, business transactions, and computer communications. Community discovery is an extensively used graph analysis kernel with rich literature for static graphs. However, community discovery in a dynamic setting is challenging for two specific reasons. Firstly, the notion of temporal community lacks a widely accepted formalization, and only limited work exists on understanding how communities emerge over time. Secondly, the added temporal dimension along with the sheer size of modern graph data necessitates new scalable algorithms. In this paper, we investigate how communities evolve over time based on several graph metrics under a temporal formalization. We compare six different algorithmic approaches for dynamic community detection for their quality and runtime. We identify that a vertex-centric (local) optimization method works as efficiently as the classical modularity-based methods. To its advantage, such local computation allows for the efficient design of parallel algorithms without incurring a significant parallel overhead. Based on this insight, we design a shared-memory parallel algorithm DyComPar , which demonstrates between 4 and 18 fold speed-up on a multi-core machine with 20 threads, for several real-world and synthetic graphs from different domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A GPU‐Accelerated Generative Adversarial Model for Causal Inference

We develop a GPU-accelerated machine learning generative adversarial model designed to facilitate causal inferences from observational data. Our model's theoretical framework is conceptualized in a manner that is amenable to being operable and scalable for high-performance computing platforms. We leverage GPU acceleration to develop a parallel evolutionary algorithm to achieve large-scale parallel computation of the model within a now widely accessible computing platform. This capability both enhances computational speedup and efficiency and also extends the use of the model to a broader range of substantive research domains while maintaining the underlying theoretical properties of the model.

GPU↗
DOE OSTI2021

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗
DOE OSTI2024

Distributed Augmentation, Hypersweeps, and Branch Decomposition of Contour Trees for Scientific Exploration

Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale using highperformance computing. To address this challenge, recent work has introduced distributed hierarchical contour trees for distributed computation and storage of contour trees. However, effective use of these distributed structures in analysis and visualization requires subsequent computation of geometric properties and branch decomposition to support contour extraction and exploration. In this work, we introduce distributed algorithms for augmentation, hypersweeps, and branch decomposition that enable parallel computation of geometric properties, and support the use of distributed contour trees as query structures for scientific exploration. Finally, we evaluate the parallel performance of these algorithms and apply them to identify and extract important contours for scientific visualization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Stochastic Vector Techniques in Ground-State Electronic Structure

Herein we review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce algorithmic complexity, facilitate efficient parallelization, simplify computational tasks, accelerate calculations, and diminish memory requirements. While their scope is vast, we limit our study to ground-state and finite temperature density functional theory (DFT) and second-order many-body perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere. We start by explaining how to use stochastic vectors in computations, characterizing the associated statistical errors. Next, we show how to estimate the electron density in DFT and discuss effective techniques to reduce statistical errors. Finally, we review the use of stochastic vectors for calculating correlation energies within the second-order Møller-Plesset perturbation theory and its finite temperature variational form. Example calculation results are presented and used to demonstrate the efficacy of the methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Accelerating a fluvial incision and landscape evolution model with parallelism

Solving inverse problems, performing sensitivity analyses, and achieving statistical rigour in landscape evolution models require running many model realizations. Parallel computation is necessary to achieve this in a reasonable time. However, no previous landscape evolution algorithm is able to leverage modern parallelism. In this report, I describe an algorithm that can utilize the parallel potential of GPUs and many-core processors, in addition to working well in serial. The new algorithm runs 43× faster (70 s vs. 3000 s on a 10,000×10,000 input) than the previous state-of-the-art and exhibits sublinear scaling with input size. I also identify key techniques for multiple flow direction routing and quickly eliminating landscape depressions and local minima. Complete, well-commented, easily adaptable source code for all versions of the algorithm is available on Github and Zenodo.

58 GEOSCIENCES↗
DOE OSTI2022

Reproduced Computational Results Report for “Ginkgo: A Modern Linear Operator Algebra Framework for High Performance Computing”

The article titled “Ginkgo: A Modern Linear Operator Algebra Framework for High Performance Computing” by Anzt et al. presents a modern, linear operator centric, C++ library for sparse linear algebra. Experimental results in the article demonstrate that Ginkgo is a flexible and user-friendly framework capable of achieving high-performance on state-of-the-art GPU architectures. In this report, the Ginkgo library is installed and a subset of the experimental results are reproduced. Specifically, the experiment that shows the achieved memory bandwidth of the Ginkgo Krylov linear solvers on NVIDIA A100 and AMD MI100 GPUs is redone and the results are compared to what presented in the published article. Upon completion of the comparison, the published results are deemed reproducible.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A parallel hierarchical blocked adaptive cross approximation algorithm

This article presents a low-rank decomposition algorithm based on subsampling of matrix entries. The proposed algorithm first computes rank-revealing decompositions of submatrices with a blocked adaptive cross approximation (BACA) algorithm, and then applies a hierarchical merge operation via truncated singular value decompositions (H-BACA). The proposed algorithm significantly improves the convergence of the baseline ACA algorithm and achieves reduced computational complexity compared to the traditional decompositions such as rank-revealing QR. Numerical results demonstrate the efficiency, accuracy, and parallel scalability of the proposed algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Designing a parallel Feel-the-Way clustering algorithm on HPC systems

This paper introduces a new parallel clustering algorithm, named Feel-the-Way clustering algorithm, that provides better or equivalent convergence rate than the traditional clustering methods by optimizing the synchronization and communication costs. Our algorithm design centers on how to optimize three factors simultaneously: reduced synchronizations, improved convergence rate, and retained same or comparable optimization cost. To compare the optimization cost, we use the Sum of Square Error (SSE) cost as the metric, which is the sum of the square distance between each data point and its assigned clusters. Compared with the traditional MPI k-means algorithm, the new Feel-the-Way algorithm requires less communications among participating processes. As for the convergence rate, the new algorithm requires fewer number of iterations to converge. As for the optimization cost, it obtains the SSE costs that are close to the k-means algorithm. In the paper, we first design the full-step Feel-the-Way k-means clustering algorithm that can significantly reduce the number of iterations that are required by the original k-means clustering method. Next, we improve the performance of the full-step algorithm by adopting an optimized sampling-based approach, named reassignment-history-aware sampling. Our experimental results show that the optimized sampling-based Feel-the-Way method is significantly faster than the widely used k-means clustering method, and can provide comparable optimization costs. More extensive experiments with several synthetic datasets and real-world datasets (e.g., MNIST, CIFAR-10, ENRON, and PLACES-2) show that the new parallel algorithm can outperform the open source MPI k-means library by up to 110% on a high-performance computing system using 4,096 CPU cores. In addition, the new algorithm can take up to 51% fewer iterations to converge than the k-means clustering algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

CG-Kit: Code Generation Toolkit for performant and maintainable variants of source code applied to Flash-X hydrodynamics simulations

CG-Kit is a new Code Generation tool-Kit that we have developed as a part of the solution for portability and maintainability for multiphysics computing applications. The development of CG-Kit is rooted in the urgent need created by the shifting landscape of high-performance computing platforms and the algorithmic complexities of a particular large-scale multiphysics application: Flash-X. To efficiently use computing resources on a heterogeneous node, an application must have a map of computation to resources and a mechanism to move the data and computation to the resources according to the map. Most existing performance portability solutions are focussed on abstracting the expression of computations so that a unified source code can be specialized to run on different resources. However, such an approach is insufficient for a code like Flash-X, which has a multitude of code components that can be assembled in various permutations and combinations to form different instances of applications. Similar challenges apply to any code that has composability, where a single specified way of apportioning work among devices may not be optimal. Additionally, use cases arise where the optimal control flow of computation may differ for different devices while the underlying numerics remain identical. This combination leads to unique challenges including handling an existing large code base in Fortran and/or C/C++, subdivision of code into a great variety of units supporting a wide range of physics and numerical methods, different parallelization techniques for distributed and shared memory systems and accelerator devices, and heterogeneity of computing platforms requiring coexisting variants of parallel algorithms. All of these challenges demand that scientific software developers apply existing knowledge about domain applications, algorithms, and computing platforms to determine custom abstractions and granularity for code generation. There is a critical lack of tools to tackle those problems. CG-Kit is designed to fill this gap by providing a user with the ability to express their desired control flow and computation-to-resource map in the form a pseudocode-like recipe. It consists of standalone tools that can be combined into highly specific and, we argue, highly effective portability and maintainability toolchains. Here we present the design of our new tools: parametrized source trees, control flow graphs, and recipes. The tools are implemented in Python. They are agnostic to the programming language of the source code targeted for code generation. In conclusion, we demonstrate the capabilities of the toolkit with two examples, first, multithreaded variants of the basic AXPY operation, and second, variants of parallel algorithms within a hydrodynamics solver, called Spark, from Flash-X that operates on block-structured adaptive meshes.

Algorithmic portability↗
DOE OSTI2020

Scalable Knowledge Graph Analytics at 136 Petaflop/s

We are motivated by newly proposed methods for data mining large-scale corpora of scholarly publications, such as the full biomedical literature, which may consist of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover how concepts relate to one another. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as one of computing all-pairs shortest paths (APSP), which becomes a significant bottleneck. In this context, we present a new high-performance algorithm and implementation of the Floyd-Warshall algorithm for distributed-memory parallel computers accelerated by GPUs, which we call DSNAPSHOT (Distributed Accelerated Semiring All-Pairs Shortest Path). For our largest experiments, we ran DSNAPSHOT on a connected input graph with millions of vertices using 4, 096nodes (24,576GPUs) of the Oak Ridge National Laboratory's Summit supercomputer system. We find DSNAPSHOT achieves a sustained performance of 136×1015 floating-point operations per second (136petaflop/s) at a parallel efficiency of 90% under weak scaling and, in absolute speed, 70% of the best possible performance given our computation (in the single-precision tropical semiring or “min-plus” algebra). Looking forward, we believe this novel capability will enable the mining of scholarly knowledge corpora when embedded and integrated into artificial intelligence-driven natural language processing workflows at scale.

Kannan, Ramakrishnan {ramki}↗
DOE OSTI2022

Detector and Beamline Simulation for Next-Generation High Energy Physics Experiments

The success of high energy physics programs relies heavily on accurate detector simulations and beam interaction modeling. The increasingly complex detector geometries and beam dynamics require sophisticated techniques in order to meet the demands of current and future experiments. Common software tools used today are unable to fully utilize modern computational resources, while data-recording rates are often orders of magnitude larger than what can be produced via simulation. In this paper, we describe the state, current and future needs of high energy physics detector and beamline simulations and related challenges, and we propose a number of possible ways to address them.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Parallel Nonnegative CP Decomposition of Dense Tensors

The CP tensor decomposition is a low-rank approximation of a tensor. We present a distributed-memory parallel algorithm and implementation of an alternating optimization method for computing a CP decomposition of dense tensors that can enforce nonnegativity of the computed low-rank factors. The principal task is to parallelize the Matricized-Tensor Times Khatri-Rao Product (MTTKRP) bottleneck subcomputation. The algorithm is computation efficient, using dimension trees to avoid redundant computation across MTTKRPs within the alternating method. Our approach is also communication efficient, using a data distribution and parallel algorithm across a multidimensional processor grid that can be tuned to minimize communication. We benchmark our software on synthetic as well as hyperspectral image and neuroscience dynamic functional connectivity data, demonstrating that our algorithm scales well to 100s of nodes (up to 4096 cores) and is faster and more general than the currently available parallel software.

Ballard, Grey↗
DOE OSTI2024

DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs

Dynamic (Temporal) graphs capture the valuable evolution of real-world systems, from the continuously evolving patterns of social interactions and genetic pathways to the dynamic fluctuations of economic forces. Detecting communities for such evolving networks poses unique challenges. Detecting and analyzing the evolution of communities within dynamic graphs unlocks valuable insights into the underlying structural and temporal patterns of real-world systems. However, the sheer volume of modern graph data and the inherent complexity of the temporal dimension pose significant challenges to scalable community detection algorithms. Addressing this gap, our work explores the limited landscape of scalable distributed-memory parallel methods specifically designed for dynamic network community detection. We propose a novel parallel algorithm, DyG-DPCD (Dynamic Graph Distributed Parallel Community Detection), to detect communities in dynamic networks using the Message Passing Interface (MPI) framework. We present a vertex-centric approach, allowing us to detect communities through local optimization. Furthermore, we enhance our baseline algorithm by incorporating three heuristics, which improve the algorithm’s performance significantly while maintaining the quality of the solutions. We demonstrate the efficiency of our algorithm by experimenting on several real-world large-scale networks with hundreds of millions of edges spanning diverse domains. Notably, DyG-DPCD achieves speedups between 25× and 30× for large networks that we experimented on using NERSC compute nodes. In conclusion, our algorithm outperforms the STINGER parallel re-agglomeration algorithm by 30×.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Xyce(™) Parallel Electronic Simulator v.7.5

The Xyce Parallel Electronic Simulator simulates electronic circuit behavior in DC, AC, HB, MPDE and transient mode using standard analog (DAE) and/or device (PDE) device models including several age and radiation aware devices. It supports a variety of computing platforms (both serial and parallel) computers. Lastly, it uses a variety of modern solution algorithms dynamic parallel load-balancing and iterative solvers.! ! Xyce is primarily used to simulate the voltage and current behavior of a circuit network (a network of electronic devices connected via a conductive network). As a tool, it is mainly used for the design and analysis of electronic circuits.! ! Kirchoff's conservation laws are enforced over a network using modified nodal analysis. This results in a set of differential algebraic equations (DAEs). The resulting nonlinear problem is solved iteratively using a fully coupled Newton method, which in turn results in a linear system that is solved by either a standard sparse-direct solver or iteratively using Trilinos linear solver packages, also developed at Sandia National Laboratories.

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