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At least 19 records

AMReX: Block-structured adaptive mesh refinement for multiphysics applications

Block-structured adaptive mesh refinement (AMR) provides the basis for the temporal and spatial discretization strategy for a number of Exascale Computing Project applications in the areas of accelerator design, additive manufacturing, astrophysics, combustion, cosmology, multiphase flow, and wind plant modeling. AMReX is a software framework that provides a unified infrastructure with the functionality needed for these and other AMR applications to be able to effectively and efficiently utilize machines from laptops to exascale architectures. AMR reduces the computational cost and memory footprint compared to a uniform mesh while preserving accurate descriptions of different physical processes in complex multiphysics algorithms. AMReX supports algorithms that solve systems of partial differential equations in simple or complex geometries and those that use particles and/or particle–mesh operations to represent component physical processes. In this article, we will discuss the core elements of the AMReX framework such as data containers and iterators as well as several specialized operations to meet the needs of the application projects. In addition, we will highlight the strategy that the AMReX team is pursuing to achieve highly performant code across a range of accelerator-based architectures for a variety of different applications.

Zhang, Weiqun↗

The Alamo multiphysics solver for phase field simulations with strong-form mechanics and block structured adaptive mesh refinement

Alamo is a high-performance scientific code that uses block-structured adaptive mesh refinement to solve such problems as: the ignition and burn of solid rocket propellant, plasticity, damage and fracture in materials undergoing loading, and the interaction of compressible flow with eroding solid materials. Alamo is powered by AMReX, and provides a set of unique methods, models, and algorithms that enable it to solve solid-mechanics problems (coupled to other physical behavior such as fluid flow or thermal diffusion) using the power of block-structured adaptive mesh refinement.

36 MATERIALS SCIENCE↗

Parthenon—a performance portable block-structured adaptive mesh refinement framework

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive mesh refinement (AMR) framework Parthenon, derived from the well-tested and widely used Athena++ astrophysical magnetohydrodynamics code, but generalized to serve as the foundation for a variety of downstream multi-physics codes. Parthenon adopts the Kokkos programming model, and provides various levels of abstractions from multidimensional variables, to packages defining and separating components, to launching of parallel compute kernels. Parthenon allocates all data in device memory to reduce data movement, supports the logical packing of variables and mesh blocks to reduce kernel launch overhead, and employs one-sided, asynchronous MPI calls to reduce communication overhead in multi-node simulations. Using a hydrodynamics miniapp, we demonstrate weak and strong scaling on various architectures including AMD and NVIDIA GPUs, Intel and AMD x86 CPUs, IBM Power9 CPUs, as well as Fujitsu A64FX CPUs. At the largest scale on Frontier (the first TOP500 exascale machine), the miniapp reaches a total of 1.7 × 10 13 zone-cycles/s on 9216 nodes (73,728 logical GPUs) at [Formula: see text] weak scaling parallel efficiency (starting from a single node). In combination with being an open, collaborative project, this makes Parthenon an ideal framework to target exascale simulations in which the downstream developers can focus on their specific application rather than on the complexity of handling massively-parallel, device-accelerated AMR.

97 MATHEMATICS AND COMPUTING↗

Structured Adaptive Mesh Refinement Adaptations to Retain Performance Portability With Increasing Heterogeneity

Adaptive mesh refinement (AMR) is an important method that enables many mesh-based applications to run at effectively higher resolution within limited computing resources by allowing high resolution only where really needed. This advantage comes at a cost, however: greater complexity in the mesh management machinery and challenges with load distribution. With the current trend of increasing heterogeneity in hardware architecture, AMR presents an orthogonal axis of complexity. Additionally, the usual techniques, such as asynchronous communication and hierarchy management for parallelism and memory that are necessary to obtain reasonable performance are very challenging to reason about with AMR. Different groups working with AMR are bringing different approaches to this challenge. Here, we examine the design choices of several AMR codes and also the degree to which demands placed on them by their users influence these choices.

42 ENGINEERING↗

The Pele Simulation Suite for Reacting Flows at Exascale

In this work, we present the Pele suite of software tools for compressible and incompressible reacting flows. The Pele suite leverages several different libraries, notably AMReX and SUNDIALS, to achieve performance portability on heterogeneous computing architectures across the supercomputing landscape. The Pele suite is comprised of PeleC, a compressible reacting flow block-structured adaptive mesh refinement solver, PeleLMeX, a low-Mach number reacting flow block-structured adaptive mesh refinement solver, Pele-Physics, a library for transport, thermodynamics, finite rate chemistry, soot, spray and radiation physics. The objective of this paper is (i) to present the code development efforts necessary to achieve highly effective and scalable applications for exascale machines and (ii) to detail the performance results of the Combustion-Pele project applications on Oak Ridge National Laboratory's Frontier. We show good weak and strong scaling results for both PeleC and PeleLMeX up to more than 50 billion cells on more than 4096 Frontier graphics processing unit nodes. We also present a capability demonstration simulation of a dual-fuel pulse compression ignition engine (six adaptive mesh refinement levels, and 60 billion cells or 2.1 trillion degrees of freedom) on Frontier, to date one of the largest simulations performed on the first exascale-class supercomputer.

adaptive mesh refinement↗

A Moving Embedded Boundary Approach for the Compressible Navier-Stokes Equations in a Block-Structured Adaptive Refinement Framework

A computational technique has been developed to perform compressible flow simulations involving moving boundaries using an embedded boundary approach within the block-structured adaptive mesh refinement (SAMR) framework of AMReX [1], [91], [92]. We leverage the SAMR capability to obtain quantitatively accurate results whilst using robust, second-order finite volume schemes. A conservative, unsplit, cut-cell approach is utilized and a ghost-cell approach is developed for computing the flux on the moving, embedded boundary faces. A third-order least-squares formulation has been developed to compute the wall velocity gradients, and was found to significantly improve the performance of the solver in terms of the quantitative comparison of surface quantities such as the skin friction coefficient. Various test cases are performed to validate the method, and compared with analytical, experimental, and other numerical results in literature. Inviscid and viscous test cases are performed that span a wide regime of flow speeds - acoustic (harmonically pulsating sphere), smooth flows (expansion fan created by a receding piston) and flows with shocks (shock-cylinder interaction, shock-wedge interaction, pitching NACA 0012 airfoil and shock-cone interaction). A closed system with moving boundaries - an oscillating piston in a cylinder, showed that the percentage error in mass within the system decreases with refinement, demonstrating that the numerical scheme is conservative with grid refinement, but is not discretely conservative. Viscous test cases involve that of a horizontally moving cylinder at Re = 40, an inline oscillating cylinder at Re = 100, and a transversely oscillating cylinder at Re = 185. The judicious use of adaptive mesh refinement with appropriate refinement criteria to capture the regions of interest leads to well-resolved flow features, and good quantitative comparison is observed with the results available in literature.

adaptive refinement↗

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↗

PeleLMeX: an AMR Low Mach Number Reactive Flow Simulation Code without level sub-cycling

PeleLMeX simulates chemically reacting low Mach number flows with block-structured adaptive mesh refinement (AMR). The code is built upon the AMReX library, which provides the underlying data structures and tools to manage and operate on them across massively parallel computing architectures. PeleLMeX algorithmic features are inherited from its predecessor PeleLM but key improvements allow representation of more complex physical processes. Together with its compressible flow counterpart PeleC, the thermo-chemistry library PelePhysics and the multi-physics library PeleMP, it forms the Pele suite of open-source reactive flow simulation codes.

97 MATHEMATICS AND COMPUTING↗

ERF: Energy Research and Forecasting

The Energy Research and Forecasting (ERF) code is a new model that simulates the mesoscale and microscale dynamics of the atmosphere using the latest high-performance computing architectures. It employs hierarchical parallelism using an MPI+X model, where X may be OpenMP on multicore CPU-only systems, or CUDA, HIP, or SYCL on GPU-accelerated systems. ERF is built on AMReX (Zhang et al., 2019, 2021), a block-structured adaptive mesh refinement (AMR) software framework that provides the underlying performance-portable software infrastructure for block-structured mesh operations. The "energy" aspect of ERF indicates that the software has been developed with renewable energy applications in mind. In addition to being a numerical weather prediction model, ERF is designed to provide a flexible computational framework for the exploration and investigation of different physics parameterizations and numerical strategies, and to characterize the flow field that impacts the ability of wind turbines to extract wind energy. The ERF development is part of a broader effort led by the US Department of Energy's Wind Energy Technologies Office.

17 WIND ENERGY↗

Adaptive Mesh Refinement Simulations for Turbulent Reacting Flow

With the increased availability of exascale computing hardware, detailed simulations of realistic devices can be performed at practically relevant time and length scales. Insights into the multiscale driving mechanisms in compressible reacting flow systems with complex geometry, such as combustors, can be used for design optimization and technology improvements. However, to effectively perform these simulations, advanced numerical algorithms must be used to maintain solution accuracy without incurring undue computational costs. PeleC, part of the Pele suite of codes, leverages block-structured adaptive mesh refinement (AMR) through the AMReX library to capture fine-scale flow features in compressible reacting flows. In this talk, we discuss recent improvements to the numerical algorithms, particularly in regard to describing flows at complex boundary structures, and PeleC's performance on exascale computing hardware. We will demonstrate that PeleC is well-suited for modern, extreme-scale, heterogenous compute platforms.

combustion↗

Early experiences on the OLCF Frontier system with AthenaPK and Parthenon–Hydro

The Oak Ridge Leadership Computing Facility (OLCF) has been preparing the nation's first exascale system, Frontier, for production and end users. Frontier is based on HPE Cray's new EX architecture and Slingshot interconnect and features 74 cabinets of optimized 3rd Gen AMD EPYC CPUs for HPC and AI and AMD Instinct 250X accelerators. As a part of this preparation, “real-world” user codes have been selected to help assess the functionality, performance, and usability of the system. This article describes early experiences using the system in collaboration with the Hamburg Observatory for two selected codes, which have since been adopted in the OLCF test harness. Experiences discussed include efforts to resolve performance variability and per-cycle slowdowns. Results are shown for a performance portable astrophysical magnetohydronamics code, AthenaPK, and a mini-application stressing the core functionality of a performance portable block-structured adaptive mesh refinement framework, Parthenon-Hydro. Here, these results show good scaling characteristics to the full system. At the largest scale, the Parthenon-Hydro miniapp reaches a total of $1.7$ $\times$ $10^{13}$ zone-cycles/s on 9216 nodes (73,728 logical GPUs) at ≈92% weak scaling parallel efficiency (starting from a single node using a second-order, finite-volume method).

97 MATHEMATICS AND COMPUTING↗

A hybrid adaptive multiresolution approach for the efficient simulation of reactive flows

Computational studies that use block-structured adaptive mesh refinement (AMR) approaches suffer from unnecessarily high mesh resolution in regions adjacent to important solution features. This deficiency limits the performance of AMR codes. In this work a novel hybrid adaptive multiresolution (HAMR) approach to AMR-based calculations is introduced to address this issue. The multiresolution (MR) smoothness indicators are used to identify regions of smoothness on the mesh where the computational cost of individual physics solvers may be decreased by replacing direct calculations with interpolation. We suggest an approach to balance the errors due to the adaptive discretization and the interpolation of physics quantities such that the overall accuracy of the HAMR solution is consistent with that of the MR-driven AMR solution. The performance of the HAMR scheme is evaluated for a range of test problems, from pure hydrodynamics to turbulent combustion.

97 MATHEMATICS AND COMPUTING↗

Emu v1.1

Emu is a particle-in-cell code for solving the neutrino quantum kinetic equations in 1, 2, or 3 spatial dimensions with arbitrary angular resolution in order to simulate neutrino flavor transformation in neutron star merger and core collapse supernova environments. Emu represents the neutrino distribution function as a set of particles, each of which represent a collection of neutrinos and antineutrinos with unique position and momentum. Each particle carries two density matrices to define the flavor state of the neutrinos and antineutrinos it represents. Emu includes the vacuum, matter, and neutrino self-interaction potentials. Emu calculates the self-interaction potential using PIC deposition and interpolation algorithms that efficiently compute the local number density and flux at particle locations. Emu is implemented in C++ and is based on the AMReX library for high-performance, block-structured adaptive mesh refinement. Emu is parallelized with MPI + OpenMP for CPUs and MPI + CUDA for GPUs.

Willcox, Donald↗

mesoflow [SWR-22-56]

Mesoflow is a continuum scale simulation tool developed specifically for modeling transport and chemistry at the mesoscale. Our solver utilizes Cartesian block-structured adaptive mesh refinement to resolve complex surface morphologies (of catalysts/biomass particles among others) directly obtained from X-ray tomography data. An immersed boundary based formulation enables rapid representation of complex geometries prevalent in most mesoporous interfaces. The solver is developed on top of open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Our flexible software framework enables integration of complex chemical mechanisms at heterogenous interfaces and time-split algorithms for circumventing highly disparate reaction and flow time-scales. Our current studies indicate a ten-fold performance gain by using graphics-processing-units (GPU) compared to a single processor for representative problem sizes (2 million cell mesh).

Sitaraman, Hariswaran↗

AMReX v2024

The software framework, AMReX, supports the development of block-structured adaptive mesh refinement (AMR) algorithms for solving systems of partial differential equations. AMR reduces the computational cost and memory footprint compared to a uniform mesh while preserving the essential local descriptions of different physical processes in complex multiphysics algorithms. AMR uses a hierarchical representation of the solution at multiple levels of resolution where the solution on each level is defined on the union of data containers at that resolution. These data containers, which represent the solution over a logically rectangular subregion of the domain, can contain field data defined on a mesh, Lagrangian particles or combinations of both. In addition to these basic data types, AMReX supports a multilevel embedded boundary representation of complex geometry; linear solvers for cell-centered and nodal data; asynchronous I/O in a native format readable by ParaView, VisIt and yt; and interfaces to hypre and PETSc solvers. AMReX enables applications to run on distributed memory architectures with multicore CPUs and with GPU accelerators. AMReX uses a lightweight abstraction layer that effectively hides the details of the architecture from the application. The framework currently supports CUDA, HIP and SYCL for GPU acceleration and OpenMP for multi-core CPU architectures.

Almgren, Ann↗

A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries

Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.

computational fluid dynamics (CFD)↗