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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Case Study of Using Kokkos and SYCLs Performance-Portable Frameworks for Milc-Dslash Benchmark on NVIDIA, AMD and Intel GPUs

Six of the top ten supercomputers in the TOP500 list from June 2021 rely on NVIDIA GPUs to achieve their peak compute bandwidth. With the announcement of Aurora, Frontier, and El Capitan, Intel and AMD have also entered the domain of providing GPUs for scientific computing. A consequence of the increased diversity in the GPU landscape is the emergence of portable programming models such as Kokkos, SYCL, OpenCL, and OpenMP, which allow application developers to maintain a single-source code across a diverse range of hardware architectures. While the portable frameworks try to optimize the compute resource usage on a given architecture, it is the programmers responsibility to expose parallelism in an application that can take advantage of thousands of processing elements available on GPUs. In this paper, we introduce a GPU-friendly parallel implementation of Milc-Dslash that exposes multiple hierarchies of parallelism in the algorithm. Milc-Dslash was designed to serve as a benchmark with highly optimized matrix-vector multiplications to measure the resource utilization on the GPU systems. The parallel hierarchies in the Milc-Dslash algorithm are mapped onto a target hardware using Kokkos and SYCL programming models. We present the performance achieved by Kokkos and SYCL implementations of Milc-Dslash on NVIDIA A100 GPU, AMD MI100 GPU, and Intel Gen9 GPU. Additionally, we compare the Kokkos and SYCL performances with those obtained from the versions written in CUDA and HIP programming models on NVIDIA A100 GPU and AMD MI100 GPU, respectively.

Dufek, Amanda S↗
DOE OSTI2020

Efficient and Flexible Hierarchical Data Layouts for a Unified Encoding of Scalar Field Precision and Resolution

To address the problem of ever-growing scientific data sizes making data movement a major hindrance to analysis, we introduce a novel encoding for scalar fields: a unified tree of resolution and precision, specifically constructed so that valid cuts correspond to sensible approximations of the original field in the precision-resolution space. Furthermore, we introduce a highly flexible encoding of such trees that forms a parameterized family of data hierarchies. We discuss how different parameter choices lead to different trade-offs in practice, and show how specific choices result in known data representation schemes such as zfp[52], idx[58], and jpeg2000 [76]. Lastly, we provide system-level details and empirical evidence on how such hierarchies facilitate common approximate queries with minimal data movement and time, using real-world data sets ranging from a few gigabytes to nearly a terabyte in size. Experiments suggest that our new strategy of combining reductions in resolution and precision is competitive with state-of-the-art compression techniques with respect to data quality, while being significantly more flexible and orders of magnitude faster, and requiring significantly reduced resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

AMM: Adaptive Multilinear Meshes

Adaptive representations are increasingly indispensable for reducing the in-memory and on-disk footprints of large-scale data. Usual solutions are designed broadly along two themes: reducing data precision, e.g., through compression, or adapting data resolution, e.g., using spatial hierarchies. Additionally, recent research suggests that combining the two approaches, i.e., adapting both resolution and precision simultaneously, can offer significant gains over using them individually. However, there currently exist no practical solutions to creating and evaluating such representations at scale. In this work, we present a new resolution-precision-adaptive representation to support hybrid data reduction schemes and offer an interface to existing tools and algorithms. Through novelties in spatial hierarchy, our representation, Adaptive Multilinear Meshes (AMM), provides considerable reduction in the mesh size. AMM creates a piecewise multilinear representation of uniformly sampled scalar data and can selectively relax or enforce constraints on conformity, continuity, and coverage, delivering a flexible adaptive representation. AMM also supports representing the function using mixed-precision values to further the achievable gains in data reduction. We describe a practical approach to creating AMM incrementally using arbitrary orderings of data and demonstrate AMM on six types of resolution and precision datastreams. By interfacing with state-of-the-art rendering tools through VTK, we demonstrate the practical and computational advantages of our representation for visualization techniques. With an open-source release of our tool to create AMM, we make such evaluation of data reduction accessible to the community, which we hope will foster new opportunities and future data reduction schemes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Progressive Tree-Based Compression of Large-Scale Particle Data

Scientific simulations and observations using particles have been creating large datasets that require effective and efficient data reduction to store, transfer, and analyze. However, current approaches either compress only small data well while being inefficient for large data, or handle large data but with insufficient compression. Toward effective and scalable compression/decompression of particle positions, we introduce new kinds of particle hierarchies and corresponding traversal orders that quickly reduce reconstruction error while being fast and low in memory footprint. Our solution to compression of large-scale particle data is a flexible block-based hierarchy that supports progressive, random-access, and error-driven decoding, where error estimation heuristics can be supplied by the user. For low-level node encoding, we introduce new schemes that effectively compress both uniform and densely structured particle distributions. Our proposed methods thus target all three phases of a tree-based particle compression pipeline, namely tree construction, tree traversal, and node encoding. In conclusion, the improved efficacy and flexibility of these methods over existing compressors are demonstrated through extensive experimentation, using a wide range of scientific particle datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Advanced Multilevel Monte Carlo Methods

This article reviews the application of some advanced Monte Carlo techniques in the context of multilevel Monte Carlo (MLMC). MLMC is a strategy employed to compute expectations, which can be biassed in some sense, for instance, by using the discretization of an associated probability law. The MLMC approach works with a hierarchy of biassed approximations, which become progressively more accurate and more expensive. Additionally, using a telescoping representation of the most accurate approximation, the method is able to reduce the computational cost for a given level of error versus i.i.d. sampling from this latter approximation. All of these ideas originated for cases where exact sampling from couples in the hierarchy is possible. This article considers the case where such exact sampling is not currently possible. We consider some Markov chain Monte Carlo and sequential Monte Carlo methods, which have been introduced in the literature, and we describe different strategies that facilitate the application of MLMC within these methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Multilevel Spectral Coarsening for Graph Laplacian Problems with Application to Reservoir Simulation

We extend previously developed two-level coarsening procedures for graph Laplacian problems written in a mixed saddle point form to the fully recursive multilevel case. The resulting hierarchy of discretizations gives rise to a hierarchy of upscaled models, in the sense that they provide approximation in the natural norms (in the mixed setting). This property enables us to utilize them in three applications: (i) as an accurate reduced model, (ii) as a tool in multilevel Monte Carlo simulations (in application to finite volume discretizations), and (iii) for providing a sequence of nonlinear operators in a full approximation scheme for solving nonlinear pressure equations discretized by the conservative two-point flux approximation. Finally, we illustrate the potential of the proposed multilevel technique in all three applications on a number of popular benchmark problems used in reservoir simulation.

multilevel Monte Carlo↗
DOE OSTI2023

Parallel Element-based Algebraic Multigrid for H (c url ) and H (div) Problems Using the ParELAG Library

This paper presents the use of element-based algebraic multigrid (AMGe) hierarchies, implemented in the ParELAG (Parallel Element Agglomeration Algebraic Multigrid Upscaling and Solvers) library, to produce multilevel preconditioners and solvers for H (c url ) and H (div) formulations. ParELAG constructs hierarchies of compatible nested spaces, forming an exact de Rham sequence on each level. This allows the application of hybrid smoothers on all levels and AMS (Auxiliary-space Maxwell Solver) or ADS (Auxiliary-space Divergence Solver) on the coarsest levels, obtaining complete multigrid cycles. Numerical results are presented, showing the parallel performance of the proposed methods. As a part of the exposition, this paper demonstrates some of the capabilities of ParELAG and outlines some of the components and procedures within the library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Open quantum systems for quarkonia

I review recent applications of the open quantum system framework in the understanding of quarkonium suppression in heavy-ion collisions, which has been used as a probe of the quark–gluon plasma for decades. The derivation of the Lindblad equations for quarkonium in both the quantum Brownian motion and the quantum optical limits and their semiclassical counterparts is explained. The hierarchy of time scales assumed in the derivation is justified from the separation of energy scales in nonrelativistic effective field theories of QCD. Physical implications of the open quantum system approach are also discussed. Finally, I list some open questions for future studies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Reducing communication in algebraic multigrid with multi-step node aware communication

Algebraic multigrid (AMG) is often viewed as a scalable [Formula: see text] solver for sparse linear systems. Yet, AMG lacks parallel scalability due to increasingly large costs associated with communication, both in the initial construction of a multigrid hierarchy and in the iterative solve phase. This work introduces a parallel implementation of AMG that reduces the cost of communication, yielding improved parallel scalability. It is common in Message Passing Interface (MPI), particularly in the MPI-everywhere approach, to arrange inter-process communication, so that communication is transported regardless of the location of the send and receive processes. Performance tests show notable differences in the cost of intra- and internode communication, motivating a restructuring of communication. In this case, the communication schedule takes advantage of the less costly intra-node communication, reducing both the number and the size of internode messages. Node-centric communication extends to the range of components in both the setup and solve phase of AMG, yielding an increase in the weak and strong scaling of the entire method.

Computer Science↗
DOE OSTI2022

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗
DOE OSTI2021

Deep reinforcement learning for dynamic control of fuel injection timing in multi-pulse compression ignition engines

Conventional compression-ignition (CI) engines have long offered high thermal efficiencies and torque across a wide range of loads, but often require extensive exhaust gas treatment that decreases efficiency to meet ever-increasing emissions regulations. One strategy to decrease emissions is to split the fuel injection into a series of smaller injections. In this paper, we explore a new way of discovering optimal control strategies for the next generation of CI engines using deep reinforcement learning (DRL). We outline a DRL procedure to maximize the weighted reward of engine work while minimizing end-of-cycle NO x emissions. Through the procedure outlined in this paper, we show that the DRL agent is able to reduce NO x emissions threefold while only decreasing network by 2%. We demonstrate the use of transfer learning (TL) across hierarchies of physical models to accelerate the learning process, making this approach feasible for a range of control problems within this space. This paper presents a framework and demonstration for using DRL to design control systems in technology areas such as multi-pulse engine control where a hierarchy of models combined with multi-objective rewards are used for optimal operation.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2026

Data for Spatial Analysis of Cell Patterning to Aid Genetic and Phenotypic Understanding of Grass Stomatal Density: A Case Study in Maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

AI/ML↗
DOE OSTI2020

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Bayesian Calibration Framework with Embedded Model Error for Model Diagnostics

We study the utility and performance of a Bayesian model error embedding construction in the context of molecular dynamics modeling of metallic alloys, where we embed model error terms in existing interatomic potential model parameters. To alleviate the computational burden of this approach, we propose a framework combining likelihood approximation and Gaussian process surrogates. Here we leverage sparse Gaussian process techniques to construct a hierarchy of increasingly accurate but more expensive surrogate models. This hierarchy is then exploited by multilevel Markov chain Monte Carlo methods to efficiently sample from the target posterior distribution. We illustrate the utility of this approach by calibrating an interatomic potential model for a family of gold-copper alloys. In particular, this case study highlights effective means for dealing with computational challenges with Bayesian model error embedding in large-scale physical models, and the utility of embedded model error for model diagnostics.

Bayesian inference↗
DOE OSTI2021

Milestone M6 Report: Reducing Excess Data Movement Part 1

This is the second in a sequence of three Hardware Evaluation milestones that provide insight into the following questions: What are the sources of excess data movement across all levels of the memory hierarchy, going out to the network fabric? What can be done at various levels of the hardware/software hierarchy to reduce excess data movement? How does reduced data movement track application performance? The results of this study can be used to suggest where the DOE supercomputing facilities, working with their hardware vendors, can optimize aspects of the system to reduce excess data movement. Quantitative analysis will also benefit systems software and applications to optimize caching and data layout strategies. Another potential avenue is to answer cost-benefit questions, such as those involving memory capacity versus latency and bandwidth. This milestone focuses on techniques to reduce data movement, quantitatively evaluates the efficacy of the techniques in accomplishing that goal, and measures how performance tracks data movement reduction. We study a small collection of benchmarks and proxy mini-apps that run on pre-exascale GPUs and on the Accelsim GPU simulator. Our approach has two thrusts: to measure advanced data movement reduction directives and techniques on the newest available GPUs, and to evaluate our benchmark set on simulated GPUs configured with architectural refinements to reduce data movement.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

On ParELAG's Parallel Element-based Algebraic Multigrid and its MFEM Miniapps for H(curl) and H(div) Problems: a report including lowest and next to the lowest order numerical results

This paper presents the utilization of element-based algebraic multigrid (AMGe) hierarchies, implemented in the ParELAG (Parallel Element Agglomeration Algebraic Multigrid Upscaling and Solvers) library, to produce multilevel preconditioners and solvers for H(curl) and H(div) formulations. This involves the construction of hierarchies of compatible nested spaces, forming an exact de Rham sequence on each level. This allows the application of hybrid smoothers on all levels and AMS (Auxiliary-space Maxwell Solver) or ADS (Auxiliary-space Divergence Solver) on the coarsest levels, obtaining complete multigrid cycles. Numerical results are presented, showing the parallel performance of the proposed methods. As a part of the exposition, this paper demonstrates some of the capabilities of ParELAG and outlines some of the components and procedures within the library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Milestone M7 Report: Reducing Excess Data Movement Part 2

This milestone evaluates techniques to measure and, if possible, reduce data movement across all levels of the memory hierarchy, focusing on CPU/GPU page level data movement and on intra-GPU memory hierarchy. We quantitatively evaluate the efficacy of the techniques in reducing data movement and measure how performance tracks data movement reduction. We study a small collection of benchmarks and proxy mini-apps that run on advanced pre-exascale GPUs and on the Accelsim GPU simulator. Our approach has two thrusts: to measure advanced data movement reduction directives and techniques on the newest available GPUs, and to evaluate our benchmark set on simulated GPUs configured with architectural refinements to reduce data movement. We primarily evaluated NVidia-based architectures due to the unavailability of AMD GPU hardware and tools until very recently.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Universal Utility Data Exchange (UUDEX) – Security and Administration: Cybersecurity of Energy Delivery Systems (CEDS) Research and Development

A critical component of the Universal Utility Data Exchange (UUDEX) approach is the integrated security contained within its processing. This document describes how that security is designed and expected to be implemented by UUDEX Implementations (U-Implementations), including the UUDEX Server (U-Server) and UUDEX Clients (U-Clients). The UUDEX security hierarchy consists of three levels: 1. The UUDEX Instance (U-Instance) itself, which sits at the top of the hierarchy and contains the U-Server, the UUDEX Identity Authority (U-Identity Authority), and the UUDEX Administrator (U-Administrator) functions; 2. A group of one or more UUDEX Participants (U-Participants) that present “organizations” that participate in the U-Instance and contains the UUDEX Administrator Participant (U-U-Administrator Participant) function; 3. A group of one or more UUDEX Endpoints (U-Endpoints) that represent the individual UUDEX Publish Clients (U-Publish Client) responsible for supplying data to the U-Instance that is consumed by UUDEX Subscriber Clients (U-Subscriber Clients). U-Endpoints can be either autonomous devices that publish and subscribe data such as data exchange servers found in supervisory control and data acquisition and energy management systems, or they can be tied to users of applications that, for example, submit DOE OE-417 disturbance reports. U-Participants and U-Endpoints can be organized into UUDEX Groups (U-Groups). Any number of U-Participants or U-Endpoints can be members of a U-Group. A given U-Participant or U-Endpoint can be a member of multiple U-Groups, but a U-Group cannot contain other U-Groups. For example, a U-Group could be created to contain all U-Participant Transmission Operators within the purview of a Reliability Coordinator, and another U-Group could be created to contain all U-Participant Generator Operators within the purview of a Reliability Coordinator. U-Participants that are both Transmission Operators and Generator Operators would be members of both U-Groups. U-Participants, U-Endpoints, and U-Groups are used in the access control structures to provide access to individual UUDEX Subjects (U-Subjects). U-Groups are created by the U-Administrator and are managed by the U-Administrator or the designated U-Group Managers. U-Endpoints can be assigned UUDEX Roles (U-Roles) that can be used to further restrict access. U-Roles are assigned to individual U-Endpoints. For example, a U-Role of “Security Analyst” could be used to restrict which U-Endpoints can publish or subscribe security incident reports and vulnerability notifications, while a U-Role of “Transmission Planner” can be used to restrict which U-Endpoints can publish power system model updates. U-Role definitions are created by the U-Administrator, but the U-Roles are assigned to U-Endpoints by their respective UUDEX Participant Administrators (U-Participant Administrator). Because all information required to make security decisions is either included within the U-Endpoint’s X.509 digital certificate or stored in a datastore on the U-Server, all security decisions are performed and enforced within the U-Server. This reduces the complexity of the U-Client code and minimizes the chance for compromise of the integrity of the UUDEX security features.

97 MATHEMATICS AND COMPUTING↗