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DOE OSTI2022

Pele: An Exascale-Ready Suite of Combustion Codes

High fidelity simulations of realistic combustion devices are extremely demanding computationally because of the requirements to capture complex fuel chemical decomposition, its intricate interactions with turbulent, often multiphase, flows, and the wide separation of space and time scales between the thin flame and the device boundaries. Software required to carry out such computations tends to be extremely complex, particularly when designed to exploit hardware accelerators, and can be difficult to port and maintain. We present Pele, a performance portable suite of tools for the simulation of combustion systems, including codes to evolve reactive multiphase configurations in the low Mach number and compressible flow regimes, along with a set of inter-compatible post processing and in situ analysis tools. The Pele suite of tools is built on top of the AMReX framework for block-structured adaptive mesh refinement, which provides efficient data structures and algorithms that enable the development of a wide variety of efficient mesh and particle based PDE integration schemes. A hierarchical MPI+X parallelism scheme supports CPU-only and accelerated architectures, where X can be OpenMP, CUDA, and HIP based approaches for intra-node computational work distribution. The algorithms and data structures underlying the Pele simulation and analysis tools are highly scalable and performant across a wide variety of high-performance computing platforms, including DOEs newest exascale-class machines, Frontier and Aurora. The simulation and analysis tools are fully documented and freely distributed as open source via GitHub. We present key algorithmic and software challenges, solution strategies, performance and resulting set of capabilities.

AMReX↗

DOE OSTI2023

Automated analysis of lattice structures using computed tomography

Systems, methods, and computer-readable media for evaluating a set of computed tomography data associated with a lattice structure. The lattice structure may be additively manufactured. The computed tomography data may be segmented using a filter for identifying blob-like structures to identify nodes present within the lattice structure. A three-dimensional path traversal is applied to volumetric data to identify a plurality of struts within the lattice structure that are compared to corresponding struts within a set if three-dimensional mesh data of the lattice structure to identify defective struts. Further, two-dimensional slices may be extracted from each of the computed tomography data and the mesh data and compared to identify one or more inconsistencies indicative of defects within the lattice structure.

Schiefelbein, Bryan E.↗

DOE OSTI2024

Automated analysis of lattice structures using computed tomography

Schiefelbein, Bryan E.↗

DOE OSTI2019

Composite matrix construction for structured grid adaptive mesh refinement

Structured-grid adaptive mesh refinement (SAMR) is an approach to mesh generation that supports structured access to data and adaptive mesh refinement for discretized partial differential equations (PDEs). Solution algorithms often require that an inverse of an operator be applied, a system of algebraic equations must be solved, and this process is often the primary computational cost in an application. SAMR is well suited to geometric multigrid solvers, which can be effective, but often do not adapt well to complex geometry including material coefficients. Algebraic multigrid (AMG) is more robust in the face of complex geometry, in both boundary conditions and internal material interfaces. AMG requires a stored matrix linearization of the operator. We discuss an approach, and an implementation in the Chombo block-structured AMR framework, for constructing composite grid matrices from a SAMR hierarchy of grids for use in linear solvers in the PETSc numerical library. We consider a case study with the Chombo-based BISICLES ice sheet modeling application.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Ume: Unstructured Mesh Explorations

Ume is an open-source collection of data structures for unstructured computational meshes and some simple algorithms that operate on them. These algorithms mimic the memory access patterns of a common class of operations found in several of the computational physics simulation codes developed at Los Alamos National Laboratory. The intent is that Ume can be used by hardware vendors to understand the memory traffic created by complex codes in a simplified environment, and to explore new means of optimization for that traffic. Ume is provided as a source-code C++ library and includes several applications that demonstrate the use of that library.

Henning, Paul↗

DOE OSTI2023

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) [SWR-23-37]

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) is an open-source computational fluid dynamics package powered by the lattice Boltzmann equations and built on AMReX. In the lattice Boltzmann method, local collisions between meso-scale fictitious particles drive the governing equations which enables MARBLES to easily simulate flow around complex and/or moving geometry without the generation of a body-conforming mesh. Using AMReX data structures and operations ensures a high level of computational performance and parallel scaling on heterogenous architectures while also naturally supporting locally enhanced grid resolution and fidelity through automatic mesh refinement. New domains and problem definitions are easily specified through an input file with examples and guidance on all options and variables provided in the MARBLES documentation.

Henry de Frahan, Marc↗

DOE OSTI2017

Metamesh, Version 1.0

Metamesh is a general-purpose C++ language library for creating data structures that represent meshes. An important difference between Metamesh and other "mesh" libraries is that Metamesh does not provide a specific mesh format, in the usual sense, or tools or a GUI by which users build specific meshes. Rather, it provides a mechanism by which mesh formats themselves can be built, based on their constituent parts and the relationships between them.Consider that a mesh in up to three space dimensions can, in principle, contain nodes (0d entities, or points), edges (1d entities), faces (2d entities), and cells (3d, or volumetric, entities). A node might be defined in terms of (x), (x,y), or (x,y,z) in Cartesian coordinates; or perhaps something else, in a different coordinate system. An edge is typically defined from two nodes; say, "edge E goes from node A=(ax,ay) to node B=(bx,by)." Faces can reasonably be defined in terms of nodes or edges, and cells in terms of nodes, edges, or faces. Note also that someone might wish to support general faces or cells, or only specific variants - say, triangular faces and tetrahedral cells, or quadrilateral faces and hexahedral cells. Or, perhaps, both triangular and quadrilateral faces (but no others), with prisms for each cell. Consider also that a mesh can have the same or a lesser dimension than that of its enclosing space. In 3d, for example, one could have a full 3d mesh, a 2d "sheet" mesh with no cells, a 1d "parametrized curve" with neither faces nor cells, or even a 1d "point cloud." And, in addition to defining a mesh scheme, a user might wish to place additional data onto one or more mesh entities. Imagine, for example, a velocity at each node, a flux across each edge or face, and a mass or average density per cell. Metamesh supports all of this, through the use of C++ class and function templates, and template metaprogramming techniques. Programmers begin with constructs that Metamesh provides (or, users can define their own), and assemble them in particular ways in order to create particular mesh formats. Metamesh then provides functionality automatically to meshes that are constructed in this manner. Finally, Metamesh provides very general functions for spinning, extruding, visualizing, and performing input/output of whatever meshes a user builds with it.

Staley, Martin↗

DOE OSTI2018

Scalable hierarchical PDE sampler for generating spatially correlated random fields using nonmatching meshes: Scalable hierarchical PDE sampler using nonmatching meshes

This work describes a domain embedding technique between two nonmatching meshes used for generating realizations of spatially correlated random fields with applications to large-scale sampling-based uncertainty quantification. The goal is to apply the multilevel Monte Carlo (MLMC) method for the quantification of output uncertainties of PDEs with random input coefficients on general and unstructured computational domains. We propose a highly scalable, hierarchical sampling method to generate realizations of a Gaussian random field on a given unstructured mesh by solving a reaction–diffusion PDE with a stochastic right-hand side. The stochastic PDE is discretized using the mixed finite element method on an embedded domain with a structured mesh, and then, the solution is projected onto the unstructured mesh. This work describes implementation details on how to efficiently transfer data from the structured and unstructured meshes at coarse levels, assuming that this can be done efficiently on the finest level. We investigate the efficiency and parallel scalability of the technique for the scalable generation of Gaussian random fields in three dimensions. An application of the MLMC method is presented for quantifying uncertainties of subsurface flow problems. Here, we demonstrate the scalability of the sampling method with nonmatching mesh embedding, coupled with a parallel forward model problem solver, for large-scale 3D MLMC simulations with up to 1.9·109 unknowns.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Accelerate microstructure evolution simulation using graph neural networks with adaptive spatiotemporal resolution

Abstract Surrogate models driven by sizeable datasets and scientific machine-learning methods have emerged as an attractive microstructure simulation tool with the potential to deliver predictive microstructure evolution dynamics with huge savings in computational costs. Taking 2D and 3D grain growth simulations as an example, we present a completely overhauled computational framework based on graph neural networks with not only excellent agreement to both the ground truth phase-field methods and theoretical predictions, but enhanced accuracy and efficiency compared to previous works based on convolutional neural networks. These improvements can be attributed to the graph representation, both improved predictive power and a more flexible data structure amenable to adaptive mesh refinement. As the simulated microstructures coarsen, our method can adaptively adopt remeshed grids and larger timesteps to achieve further speedup. The data-to-model pipeline with training procedures together with the source codes are provided.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Axom

The Axom library consists of n collection of software components that provide core computer science infrastructure capabilities that can be shared by diverse high performance computing (HPC) applications. The current set of capabilities that Axom provides includes: Customizable support for error/warning and diagnostic message reporting and coordination among components of integrated applications (e.g., physics packages, libraries, etc.); Scalable parallel aggregation and filtering of message logging; In memory datastore for hierarchical, mesh-aware simulation data. The datastore supports data description, allocation, deallocation. parallel l/0, etc; Mesh data model abstractions that enable the development of mesh-based computational algorithms that work with many diverse, application· specific mesh types; and Computational geometry primitives for developing high performance parallel algorithms based on spatial geometry and meshes, e.g., spatial acceleration data structures, sets, maps, relations, etc.

Hornung, RichardD.↗

DOE OSTI2024

Offshore Wind ENergy Simulation Toolkit (OWENS)

SAND2021-2751 O The Offshore Wind ENergy Simulation Toolkit (OWENS) is a collection of aerodynamic, structural, hydrodynamic, drivetrain, controls, composite structure and mesh preprocessing, and data postprocessing. OWENS is primarily an ontology, or glue code, pulling together many open-source and Sandia-developed libraries to model the aero-servo-hydro-elastic physics of wind and marine energy turbines. The toolkit’s intended use is for arbitrary aeroelastic rotor configurations analysis including vertical-axis wind turbines, horizontal-axis wind turbines, and analogous marine energy applications for fixed-bottom and floating configurations. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525

Owens, Brian↗

DOE OSTI2021

PUMIPic: A mesh-based approach to unstructured mesh Particle-In-Cell on GPUs

Unstructured mesh particle-in-cell, PIC, simulations executing on the current and next generation of massively parallel systems require new methods for both the mesh and particles to achieve performance and scalability on GPUs. The traditional approach to implementing PIC simulations defines data structures and algorithms in terms of particles with a full copy of the unstructured mesh on every process. To effectively scale the unstructured mesh and particles, mesh-based PIC uses the unstructured mesh as the predominant data structure with the particles stored in terms of the mesh entities. Here, this paper details the PUMIPic library, a framework for developing efficient and performance-portable mesh-based PIC simulations on GPU systems. A pseudo physics simulation based on a five-dimensional gyro-kinetic code for modeling plasma physics is used to examine the performance of PUMIPic. Scaling studies of the unstructured mesh partition and number of particles are performed up to 4096 nodes of the Summit system at Oak Ridge National Laboratory. The studies show that mesh-based PIC can utilize a partitioned mesh and maintain scaling up to system limitations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

FunMC^2: A Filter for Uncertainty Visualization of Marching Cubes on Multi-Core Devices

Visualization is an important tool for scientists to extract understanding from complex scientific data. Scientists need to understand the uncertainty inherent in all scientific data in order to interpret the data correctly. Uncertainty visualization has been an active and growing area of research to address this challenge. Algorithms for uncertainty visualization can be expensive, and research efforts have been focused mainly on structured grid types. Further, support for uncertainty visualization in production tools is limited. In this paper, we adapt an algorithm for computing key metrics for visualizing uncertainty in Marching Cubes (MC) to multi-core devices and present the design, implementation, and evaluation for a Filter for uncertainty visualization of Marching Cubes on Multi-Core devices (FunMC2). FunMC2 accelerates the uncertainty visualization of MC significantly, and it is portable across multi-core CPUs and GPUs. Evaluation results show that FunMC2 based on OpenMP runs around 11× to 41× faster on multi-core CPUs than the corresponding serial version using one CPU core. FunMC2 based on a single GPU is around 5× to 9× faster than FunMC2 running by OpenMP. Moreover, FunMC2 is flexible enough to process ensemble data with both structured and unstructured mesh types. Furthermore, we demonstrate that FunMC2 can be seamlessly integrated as a plugin into ParaView, a production visualization tool for post-processing.

Wang, Jay↗

DOE OSTI2020

Design and Testing of the Address in Real-Time Data Driver Card for the Micromegas Detector of the ATLAS New Small Wheel Upgrade

The Address in Real Time Data Driver Card (ADDC) is designed to transmit the trigger data in the Micro-Mesh Gaseous Structure (Micromegas) detector of the ATLAS New Small Wheel (NSW) upgrade. The Address in Real Time (ART) signals are generated by the front-end ASIC, named VMM chip, to indicate the address of the first above-threshold event. A custom ASIC (ART ASIC) is designed to receive the ART signals from the VMM chip and implement the hit-selection. The processed data from the ART ASIC will be transmitted out of the NSW through the GBTx serializer, the unidirectional Versatile Twin Transmitter (VTTx) and fiber optical links. The ART signal is critical for the ATLAS experiment trigger selection thus the performance and stability of the ADDC is very important. To ensure extensive testing of the ADDC, an FPGA Mezzanine Card (FMC) based testing platform and a special designed firmware/software are developed. We find that this test platform works with the commercial Xilinx VC707 FPGA development kit, independent of the other electronics of the NSW it can test all the functions of the ADDC and its long-term stability. This paper will introduce the design, testing procedure and results of the ADDC and the FMC testing platform.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Array-based Hierarchical Mesh Generation in Parallel

In this paper, we describe an array-based hierarchical mesh generation capability through uniform refinement of unstructured meshes for efficient solution of PDE's using finite element methods and multigrid solvers. A multi-degree, multi-dimensional and multi-level framework is designed to generate the nested hierarchies from an initial mesh that can be used for a number of purposes such as multi-level methods to generating large meshes. The capability is developed under the parallel mesh framework “Mesh Oriented dAtaBase” a.k.a MOAB. We describe the underlying data structures and algorithms to generate such hierarchies and present numerical results for computational efficiency and mesh quality. In conclusion, we also present results to demonstrate the applicability of the developed capability to a multigrid finite-element solver.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Persistent Octrees for Parallel Mesh Refinement Through Non-Volatile Byte-Addressable Memory

We report that octree-based mesh adaptation has enabled simulations of complex physical phenomena. Existing meshing algorithms were proposed with the assumption that computer memory is volatile. Consequently, for failure recovery, the in-core algorithms need to save memory states as snapshots with slow file I/Os. The out-of-core algorithms store octants on disks for persistence. However, neither of them was designed to leverage unique characteristics of non-volatile byte-addressable memory (NVBM). In this paper, we propose a novel data structure Distributed Persistent Merged octree (DPM-octree) for both meshing and in-memory storage of persistent octrees using NVBM. It is a multi-version data structure and can recover from failures using its earlier persistent version stored in NVBM. In addition, we design a feature-directed sampling approach to help dynamically transform the DPM-octree layout for reducing NVBM-induced memory write latency. DPM-octree uses parity trees which are created using erasure coding and stored in NVBM to support low-latency in-memory octant recovery after data loss. DPM-octree has been successfully integrated with Gerris software for simulation of fluid dynamics. Finally, our experimental results with real-world scientific workloads show that DPM-octree scales up to 1.1 billion mesh elements with 1000 processors on the Titan supercomputer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to farming, forest management and climate change. X-ray computed tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and our own code was used to noninvasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure at 31µm resolution, and extract quantitative information (root volume and surface area) from the 3D data, respectively. Based on the mesh generated from the root structure, computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soil hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. The flow variability and soil water distributions under different scenarios were investigated. Parameterizations were evaluated to show their impacts on the average conductivity. The pore-scale modeling approach provides realistic simulations of rhizosphere flow processes and provides useful information that can be linked to upscaled models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Sierra/SD – User’s Guide for NasGen – 5.20

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗