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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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DOE OSTI2021

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

PETSc/TAO Users Manual: Revision 3.18

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.20)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.23

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

PETSc/TAO Users Manual Revision 3.25

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Medial axis and local thickness computation using the Fast Sweeping Method

This report describes an efficient and robust voxel-based methodology for computing the medial axis, local thickness, and distance-to-skeleton of arbitrary three-dimensional geometries. It is assumed that the object can be represented by an exact or approximate signed distance function on a discrete grid. The gradient of such function is used to formulate a hyperbolic partial differential equation (PDE) that models the collapse of the position vector in space. By exploiting the causality property of the PDE, the Fast Sweeping Method is able to obtain the solution in a finite number of sweeps independent of the mesh resolution. The intersection of characteristic lines leads to the formation of shocks and a discrete bisector function is used to identify the medial axis. The same PDE approach is used to compute the local thickness inside the object and obtain the distance-to-skeleton field. Multiple examples are given in two and three dimensions along with a resolution study. The methodology has optimal complexity and yields subsecond computational times for geometries with over a million zones on a single core. The methodology is also capable of parallelization across shared and distributed memory architectures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

A second-order distributed memory parallel fast sweeping method for the Eikonal equation

The Eikonal equation is used to calculate wave propagation and distance fields, and due to its complexity requires numerical treatment for its solution. In this work, we present a second-order distributed memory parallel fast sweeping method. The second-order solution switches on a two-point stencil when two upwind points are available, and reverts to first-order otherwise. In all examples, the second-order method improves the solution over the first-order, allowing for significant savings in memory while achieving the same accuracy. Parallelization over distributed memory saw good weak scaling with optimal convergence. The computational time for second-order was approximately 2.5 times slower than first-order, where the largest amount of mesh points ran on 144 cores (512 GB) was ≈20 billion. The savings in memory from the second-order method combined with the distributed memory algorithm result in the ability to solve problems much larger than are possible with the serial first-order method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Programming approaches for scalability, performance, and portability of combustion physics codes

Here, this paper presents the process, strategy, and results associated with porting a typical combustion physics flow solver to current state-of-the-art and future massively-parallel computer architectures. Major focus is placed on the distinct algorithmic structure of these types of codes and how it can be integrated with modern programming paradigms for heterogeneous platforms (i.e., distributed many-core systems with accelerators). An end-to-end case study is presented that exemplifies the process in a generic manner, which then serves as a clear guide with respect to the strategy and best practices leading to a robust and adaptable framework that performs well, is durable over time, is portable, and requires minimal human-effort. This end is accomplished beginning with the use of a mature, validated, structured, multiblock code framework optimized for application of both Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS). This code has been ported to a variety of platforms over the past decade, including most recently the Oak Ridge Leadership Computing Facility’s “Summit” Platform. The experience gained on these multiple platforms provides general insights and thus the results presented are not specific to any one code or platform other than the overarching trend toward distributed many-core systems with accelerators in order to move toward exascale performance. The resultant performance and scalability of the ported code is demonstrated on a real-world application; a state-of-the-art rotating detonation rocket engine simulation that matches the complex geometry and boundary conditions imposed as part of a companion experimental campaign.

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 OSTI2023

DGaaS: GPU as a Service on Distributed Computing System

In the rapidly evolving landscape of scientific computing, Graphics Processing Units (GPUs) have become indispensable for their unparalleled ability to handle parallel tasks in complex calculations, simulations, and data analysis. Their utility is further magnified in machine learning and AI applications, where they significantly accelerate model training and predictive analytics. Within this context, the Triton Inference Server emerges as a pivotal open-source tool, specializing in AI inferencing and optimizing GPU utilization across various platforms and frameworks. This paper presents an in-depth study on distributed High Throughput Computing (HTC), specifically focusing on the HTCondor framework and its resource provisioning tools, GlideinWMS and HEPCloud. These systems enable large-scale scientific experiments like CMS and DUNE to efficiently access and utilize vast computational resources. The paper explores the core architectural components of GlideinWMS, including jobs, user pools, and worker nodes, and discusses their integration with GPUs and the Triton server. The primary aim of this research is to develop a solution that optimizes GPU utilization by leveraging Glideins and containers. This approach allows computational jobs, particularly those involving AI models, to use GPUs only when essential, thereby facilitating efficient sharing of limited GPU resources. To validate this architecture, the study conducted three key tests involving custom scripts, container-based servers, and Triton server deployments. However, the study faces challenges, notably in locating the Triton server and ensuring secure remote access. To address these issues, future work will focus on developing a proxy mechanism and enhancing security protocols. In conclusion, this study offers a comprehensive roadmap for effective and efficient GPU utilization in distributed High Throughput Computing. It aims to contribute significantly to the scientific community by solving pressing problems and implementing robust solutions in collaboration with the GlideinWMS and HEPCloud teams. The research sets the stage for a more efficient, scalable, and cost-effective paradigm in scientific computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A Sparse Distributed Gigascale Resolution Material Point Method

In this paper, we present a four-layer distributed simulation system and its adaptation to the Material Point Method (MPM). The system is built upon a performance portable C++ programming model targeting major High-Performance-Computing (HPC) platforms. A key ingredient of our system is a hierarchical block-tile-cell sparse grid data structure that is distributable to an arbitrary number of Message Passing Interface (MPI) ranks. We additionally propose strategies for efficient dynamic load balance optimization to maximize the efficiency of MPI tasks. Our simulation pipeline can easily switch among backend programming models, including OpenMP and CUDA, and can be effortlessly dispatched onto supercomputers and the cloud. Finally, we construct benchmark experiments and ablation studies on supercomputers and consumer workstations in a local network to evaluate the scalability and load balancing criteria. We demonstrate massively parallel, highly scalable, and gigascale resolution MPM simulations of up to 1.01 billion particles for less than 323.25 seconds per frame with 8 OpenSSH-connected workstations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Scale-up Unlearnable Examples Learning with High-performance Computing

Recent advancements in AI models, like ChatGPT, are structured to retain user interactions, which could inadvertently include sensitive healthcare data. In the healthcare field, particularly when radiologists use AI-driven diagnostic tools hosted on online platforms, there is a risk that medical imaging data may be repurposed for future AI training without explicit consent, spotlighting critical privacy and intellectual property concerns around healthcare data usage. Addressing these privacy challenges, a novel approach known as Unlearnable Examples (UEs) has been introduced, aiming to make data unlearnable to deep learning models. A prominent method within this area, called Unlearnable Clustering (UC), has shown improved UE performance with larger batch sizes but was previously limited by computational resources (e.g., a single workstation). To push the boundaries of UE performance with theoretically unlimited resources, we scaled up UC learning across various datasets using Distributed Data Parallel (DDP) training on the Summit supercomputer. Our goal was to examine UE efficacy at high-performance computing (HPC) levels to prevent unauthorized learning and enhance data security, particularly exploring the impact of batch size on UE’s unlearnability. Utilizing the robust computational capabilities of the Summit, extensive experiments were conducted on diverse datasets such as Pets, MedMNist, Flowers, and Flowers102. Our findings reveal that both overly large and overly small batch sizes can lead to performance instability and affect accuracy. However, the relationship between batch size and unlearnability varied across datasets, highlighting the necessity for tailored batch size strategies to achieve optimal data protection. The use of Summit’s high-performance GPUs, along with the efficiency of the DDP framework, facilitated rapid updates of model parameters and consistent training across nodes. Our results underscore the critical role of selecting appropriate batch sizes based on the specific characteristics of each dataset to prevent learning and ensure data security in deep learning applications. The source code is publicly available at https: // github. com/ hrlblab/ UE_ HPC .

Zhu, Yanfan [Vanderbilt University, Nashville, TN,↗

DOE OSTI2021

FTK: A Simplicial Spacetime Meshing Framework for Robust and Scalable Feature Tracking

In this work, we present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

New Results on Communication- and Memory-Aware Load Balancing Model and Algorithms

While load balancing in distributed-memory computing has been well-studied, we present an innovative approach to this problem: a unified, reduced-order model that combines three key components to describe “work” in a distributed system: computation, communication, and memory. Our model enables an optimizer to explore complex tradeoffs in task placement, such as augmented parallelism, at the expense of data replication increasing memory usage. We propose a fully distributed, heuristic-based load balancing optimization algorithm, and demonstrate that it quickly finds close-to-optimal solutions. We formalize the complex optimization problem as a mixed-integer linear program, and compare it to our strategy. Finally, we show that when applied to an electromagnetics code, our approach obtains up to 2.3x speedups for the imbalanced execution.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Simulating the Impact of Dynamic Rerouting on Metropolitan-scale Traffic Systems

The rapid introduction of mobile navigation aides that use real-time road network information to suggest alternate routes to drivers is making it more difficult for researchers and government transportation agencies to understand and predict the dynamics of congested transportation systems. Computer simulation is a key capability for these organizations to analyze hypothetical scenarios; however, the complexity of transportation systems makes it challenging for them to simulate very large geographical regions, such as multi-city metropolitan areas. In this article, we describe enhancements to the Mobiliti parallel traffic simulator to model dynamic rerouting behavior with the addition of vehicle controller actors and vehicle-to-controller reroute requests. The simulator is designed to support distributed-memory parallel execution using discrete event simulation and be scalable on high-performance computing platforms. We demonstrate the potential of the simulator by analyzing the impact of varying the population penetration rate of dynamic rerouting on the San Francisco Bay Area road network. Using high-performance parallel computing, we can simulate a day in the San Francisco Bay Area with 19 million vehicle trips with 50 percent dynamic rerouting penetration over a road network with 0.5 million nodes and 1 million links in less than three minutes. We present a sensitivity study on the dynamic rerouting parameters, discuss the simulator’s parallel scalability, and analyze system-level impacts of changing the dynamic rerouting penetration. Furthermore, we examine the varying effects on different functional classes and geographical regions and present a validation of the simulation results compared to real-world data.

97 MATHEMATICS AND COMPUTING↗