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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Application Experiences on a GPU-Accelerated Arm-based HPC Testbed

This paper assesses and reports the experience of ten teams working to port, validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC Developer Kit systems, each one equipped with a server-class Arm CPU from Ampere Computing and two data center GPUs from NVIDIA Corp. The systems are connected together using InfiniBand interconnect. The selected applications and mini-apps are written using several programming languages and use multiple accelerator-based programming models for GPUs such as CUDA, OpenACC, and OpenMP offloading. Working on application porting requires a robust and easy-to-access programming environment, including a variety of compilers and optimized scientific libraries. The goal of this work is to evaluate platform readiness and assess the effort required from developers to deploy well-established scientific workloads on current and future generation Arm-based GPU-accelerated HPC systems. The reported case studies demonstrate that the current level of maturity and diversity of software and tools is already adequate for large-scale production deployments.

Elwasif, Wael↗
DOE OSTI2026

thornado+FLASH-X: A Hybrid Discontinuous Galerkin–Implicit-explicit and Finite-volume Framework for Neutrino-radiation Hydrodynamics in Core-collapse Supernovae

We present neutrino-transport algorithms implemented in the toolkit for high-order neutrino-radiation hydrodynamics (thornado) and their coupling to self-gravitating hydrodynamics within the adaptive mesh refinement–based multiphysics simulation framework FLASH-X. thornado, developed primarily for simulations of core-collapse supernovae (CCSNe), employs a spectral, six-species two-moment formulation with algebraic closure and special-relativistic observer corrections accurate to $\mathcal{O}(v/c)$, and uses discontinuous Galerkin (DG) methods for phase-space discretization combined with implicit-explicit time stepping. A key development is a nonlinear neutrino–matter coupling algorithm based on nested fixed-point iteration with Anderson acceleration, enabling fully implicit treatment of collisional processes, including energy-coupling interactions such as neutrino–electron scattering and pair production. Coupling to finite-volume (FV) hydrodynamics is achieved through a hybrid DG-FV representation of the fluid variables and operator-split evolution within FLASH-X. The implementation is verified using basic transport tests with idealized opacities and relaxation and deleptonization problems with tabulated microphysics. Spherically symmetric CCSN simulations demonstrate accuracy and robustness of the coupled scheme, including close agreement with the CCSN simulation code Chimera. An axisymmetric CCSN simulation further demonstrates the viability of DG-based neutrino transport for multidimensional supernova modeling within FLASH-X. thornado’s neutrino-transport solver is GPU-enabled using OpenMP offloading or OpenACC, and all CCSN applications included in this work use the GPU implementation. Together, these results establish a foundation for future enhancements in physics fidelity, numerical algorithms, and computational performance, for increasingly realistic large-scale CCSN simulations.

Endeve, Eirik [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2022

An OpenMP GPU-offload implementation of a non-equilibrium solidification cellular automata model for additive manufacturing

Here, in this paper, performance strategies on GPU-based HPC platforms of a cellular automata (CA) simulation code for non-equilibrium solidification, including nucleation, grain growth, solute partitioning and transport for the metal additive manufacturing (AM) process are investigated using OpenMP 4.5. To accurately report the speed-up for multicore CPUs and GPUs, a rigorous performance analysis employed optimizations appropriate for both CPU-only code (baseline) and GPU offload codes for an isothermal test problem. The performance results on Summit at the Oak Ridge Leadership Computing Facility indicate that using a precomputed list of interface cells significantly decreased the wall-clock time on GPUs. The speedup due to GPU acceleration was evaluated for a full Summit node and measured to be 1.8X when comparing a 6 MPI tasks run with 6 GPUs versus 36 MPI tasks on the CPU only. That speed-up was found to be 7.9X when comparing 6 MPI tasks with 6 GPUs versus the 6 MPI tasks running on the CPU only. Performance measurements showed that system total time is almost constant for runs with more than 96 MPI tasks (or GPUs), indicating that the GPU-accelerated code showed an excellent weak scaling performance. Finally, a rapid directional solidification problem was considered to demonstrate the CA code capability on Summit. It was found that a mesh size of at least 0.05 μm is recommended for the AM-like simulations in order to obtain accurate elongated grain microstructure and elongated subgrain features, which are in qualitative good agreement with experimental data. The results presented in this study indicate that the performance strategies on GPU-based HPC platforms for the CA code are appropriate for novel HPC exascale platforms.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

Godoy, William↗
DOE OSTI2024

Large language model evaluation for high–performance computing software development

We apply AI-assisted large language model (LLM) capabilities of GPT-3 targeting high-performance computing (HPC) kernels for (i) code generation, and (ii) auto-parallelization of serial code in C ++, Fortran, Python and Julia. Our scope includes the following fundamental numerical kernels: AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG, and language/programming models: (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). Kernel implementations are generated using GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code given simple + + prompt variants. To quantify and compare the generated results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. For auto-parallelization, we use ChatGPT interactively giving simple prompts as in a dialogue with another human including simple “prompt engineering” follow ups. Results suggest that correct outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding language keywords, while Julia prompts perform acceptably well for its Threads and CUDA.jl programming models. Finally, we expect to provide an initial quantifiable point of reference for code generation in each programming model using a state-of-the-art LLM. Overall, understanding the convergence of LLMs, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

OpenMP Target Task: Tasking and Target Offloading on Heterogeneous Systems

This work evaluated the use of OpenMP tasking with target GPU offloading as a potential solution for programming productivity and performance on heterogeneous systems. Also, it is proposed a new OpenMP specification to make the implementation of heterogeneous codes simpler by using OpenMP target task, which integrates both OpenMP tasking and target GPU offloading in a single OpenMP pragma. As a test case, the authors used one of the most popular and widely used Basic Linear Algebra Subprogram Level-3 routines: triangular solver (TRSM). To benefit from the heterogeneity of the current high-performance computing systems, the authors propose a different parallelization of the algorithm by using a nonuniform decomposition of the problem. This work used target GPU offloading inside OpenMP tasks to address the heterogeneity found in the hardware. This new approach can outperform the state-of-the-art algorithms, which use a uniform decomposition of the data, on both the CPU-only and hybrid CPU-GPU systems, reaching speedups of up to one order of magnitude. The performance that this approach achieves is faster than the IBM ESSL math library on CPU and competitive relative to a highly optimized heterogeneous CUDA version. One node of Oak Ridge National Laboratory’s supercomputer, Summit, was used for performance analysis.

Valero Lara, Pedro↗
DOE OSTI2023

Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions

Here, a framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree–Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70–569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303–1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ~67,000 basis functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Outcomes of OpenMP Hackathon: OpenMP Application Experiences with the Offloading Model (Part I)

This paper reports on experiences gained and practices adopted when using the latest features of OpenMP to port a variety of HPC applications and mini-apps based on different computational motifs (BerkeleyGW, WDMApp/XGC, GAMESS, GESTS, and GridMini) to accelerator-based, leadership-class, high-performance supercomputer systems at the Department of Energy. As recent enhancements to OpenMP become available in implementations, there is a need to share the results of experimentation with them in order to better understand their behavior in practice, to identify pitfalls, and to learn how they can be effectively deployed in scientific codes. Additionally, we identify best practices from these experiences that we can share with the rest of the OpenMP community.

Chapman, Barbara↗
DOE OSTI2021

Outcomes of OpenMP Hackathon: OpenMP Application Experiences with the Offloading Model (Part II)

This paper reports on experiences gained and practices adopted when using the latest features of OpenMP to port a variety of HPC applications and mini-apps based on different computational motifs (BerkeleyGW, WDMApp/XGC, GAMESS, GESTS, and GridMini) to accelerator-based, leadership-class, high-performance supercomputer systems at the Department of Energy. As recent enhancements to OpenMP become available in implementations, there is a need to share the results of experimentation with them in order to better understand their behavior in practice, to identify pitfalls, and to learn how they can be effectively deployed in scientific codes. Additionally, we identify best practices from these experiences that we can share with the rest of the OpenMP community.

Chapman, Barbara↗
DOE OSTI2023

Acceleration of the Parameterization of Unified Microphysics Across Scales (PUMAS) on the Graphics Processing Unit (GPU) With Directive-Based Methods

Cloud microphysics is one of the most time-consuming components in a climate model. In this study, we port the cloud microphysics parameterization in the Community Atmosphere Model (CAM), known as Parameterization of Unified Microphysics Across Scales (PUMAS), from CPU to GPU to seek a computational speedup. The directive-based methods (OpenACC and OpenMP target offload) are determined as the best fit specifically for our development practices, which enable a single version of source code to run either on the CPU or GPU, and yield a better portability and maintainability. Their performance is first examined in a PUMAS stand-alone kernel and the directive-based methods can outperform a CPU node as long as there is enough computational burden on the GPU. A consistent behavior is observed when we run PUMAS on the GPU in a practical CAM simulation. A 3.6× speedup of the PUMAS execution time, including data movement between CPU and GPU, is achieved at a coarse horizontal resolution (8 NVIDIA V100 GPUs against 36 Intel Skylake CPU cores). This speedup further increases up to 5.4× at a high resolution (24 NVIDIA V100 GPUs against 108 Intel Skylake CPU cores), which highlights the fact that GPU favors larger problem size. This study demonstrates that using GPU in a CAM simulation can save noticeable computational costs even with a small portion of code being GPU-enabled. Therefore, we are encouraged to port more parameterizations to GPU to take advantage of its computational benefit.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

GenASiS Mathematics: Object-oriented manifolds, operations, and solvers for large-scale physics simulations (version 2)

We report GenASiS Mathematics provides modern Fortran classes furnishing extensible object-oriented functionality for the solution of fields governed by selected partial differential equations. The initial release included extensible object-oriented implementations of simple meshes and the evolution of generic conserved currents thereon. This revision - Version 2 of Mathematics - includes significant reorganization and streamlining of these classes, higher-order reconstruction by a different method, a Poisson solver, coarsening to avoid Courant time step limitations near coordinate singularities, and the offloading of computational kernels to GPUs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs

Computational bioinformatics and biomedical applications frequently contain heterogeneously sized units of work or tasks, for instance due to variability in the sizes of biological sequences and molecules. Variable-sized workloads lead to load imbalances in parallel implementations which detract from efficiency and performance. Many modern computing resources now have multiple graphics processing units(GPUs) per computer for acceleration. These multiple GPU resources need to be used efficiently through balancing of workloads across the GPUs. OpenMP is a portable directive-based parallel programming API used ubiquitously in bioscience applications to program CPUs; recently, the use of OpenMP directives for GPU acceleration has become possible. Here, motivated by experiences with imbalanced loads in GPU-accelerated bioinformatics applications, we address the load balancing problem using OpenMP task-to-GPU scheduling combined with OpenMP GPU offloading for multiply heterogeneous workloads – loads with both variable input sizes, and simultaneously, variable convergence rates for algorithms with a stochastic component – scheduled across multiple GPUs. We aim to develop strategies which are both easy to use and have lower overheads, and may be incorporated incrementally in existing programs which already make use of OpenMP for CPU-based threading in order to make use of multi-GPU computers. We test different combinations of input size variability and convergence rate variability, and characterize the effects of these different scenarios on the performance of scheduling strategies across multiple GPUs with OpenMP. We present several dynamic scheduling solutions for different parallel patterns, explore optimizations, and provide publicly available example computational kernels to make these strategies easy to use in programs. This work will enable application developers to efficiently and easily use multiple GPUs for imbalanced workloads found in bioinformatics and biomedical applications.

Thavappiragasam, Mathialakan↗
DOE OSTI2024

Runtime performance of a GAMESS quantum chemistry application offloaded to GPUs

Summary Computational chemistry is at the forefront of solving urgent societal problems, such as polymer upcycling and carbon capture. The complexity of modeling these processes at appropriate length and time scales is mainly manifested in the number and types of chemical species involved in the reactions and may require models of several thousand atoms and large basis sets to accurately capture the chemical complexity and heterogeneity in the physical and chemical processes. The quantum chemistry package General Atomic and Molecular Electronic Structure System (GAMESS) has a wide array of methods that can efficiently and accurately treat complex chemical systems. In this work, we have used the GAMESS Effective Fragment Molecule Orbital (EFMO) method for electronic structure calculation of a challenging mesoporous silica nanoparticle (MSN) model surrounded by about 4700 water molecules to investigate the strong scaling and GPU offloading on hybrid CPU‐GPU nodes. Experiments were performed on the Perlmutter platform at the National Energy Research Scientific Computing Center. Good strong scaling and load balancing have been observed on up to 88 hybrid nodes for different settings of the execution parameters for the calculation considered here. When GPUs are oversubscribed by offloading work from multiple CPU processes, using the NVIDIA multi‐process service (MPS) has consistently reduced time to solution and energy consumed. Additionally, for some configuration parameter settings, oversubscription with MPS improved performance by up to 5.8% over the case without oversubscription.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Uncovering grain and subgrain microstructure at the scale of additive manufacturing melt tracks with a scalable cellular automaton solidification model

Metal additive manufacturing, characterized by rapid solidification, yields refined grains with a distinctive cellular subgrain microstructure that plays a pivotal role in determining material properties. Due to the significant computational expense demanded to simulate the required physics with submicron spatial resolution, their numerical simulations have been limited to proof-of-concept studies to either 2D or small subregions of a melt pool. In this study, an open-source, scalable, solidification code, muMatScale, based on the cellular automaton method, has been developed to predict the grain and the underlying subgrain microstructure over an entire melt pool. The model incorporates flexible parallelization schemes, utilizing MPI and OpenMP GPU Offloading, in addition to appropriate multi-physics specific to non-equilibrium rapid solidification in AM. The impact of nucleation parameters on grain microstructures was investigated with a focus on grain size variations and morphology transitions. With selected nucleation parameters, the simulation predicted the grain size, subgrain morphology, crystallographic orientation, and microsegregation aligned with experimental measurements. The model demonstrates that epitaxial grain growth is a dominant factor at the melt pool boundary, influencing grain size variation under different grain sizes in the build plate while maintaining consistent primary dendrite arm spacing under identical thermal conditions. Here, the highly efficient numerical model enables large-scale simulations with a spatial resolution of 100 nm or less, unveiling unprecedented insights into thermal and solutal diffusion driven grain growth, and the subgrains with microsegregation within grains in 3D across scales. muMatScale will enable the linking of submicron length-scale microstructure to part-level material behavior by investigating fundamental solidification problems at the intercellular scale in many-track and many-layer builds.

36 MATERIALS SCIENCE↗
DOE OSTI2022

GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations (Version 4)

GenASiS Basics provides modern Fortran classes furnishing extensible object-oriented utilitarian functionality for large-scale physics simulations on distributed memory supercomputers. This functionality includes physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Herein, this revision—Version 4 of Basics—includes a name change and additions to functionality, including the facilitation of direct communication between GPUs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations

The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers. The results show that DC can speed up the Fock build by 3.0× compared with that of the OTO model. Finally, with similar offloading efforts, DC is a compelling programming model for offloading Fortran applications to GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?

High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking programs. Both cloud and high-performance computing (HPC) resources have been used for large screens with molecular docking programs; while NVIDIA GPUs have dominated cloud and HPC resources, new vendors such as AMD and Intel are now entering the field, creating the problem of software portability across different GPUs. Ideally, software productivity could be maximized with portable programming models that are able to maintain high performance across architectures. While in many cases compiler directives have been used as an easy way to offload parallel regions of a CPU-based program to a GPU accelerator, they may also be an attractive programming model for providing portability across different GPU vendors, in which case the porting process may proceed in the reverse direction: from low-level, architecture-specific code to higher-level directive-based abstractions. MiniMDock is a new mini-application (miniapp) designed to capture the essential computational kernels found in molecular docking calculations, such as are used in phar-maceutical drug discovery efforts, in order to test different solutions for porting across GPU architectures. Here we extend MiniMDock to GPU offloading with OpenMP directives, and compare to performance of kernels using CUDA and HIP on NVIDIA and AMD GPUs, respectively, as well as across different compilers, exploring performance bottlenecks. We document this reverse-porting process, from highly optimized device code to a higher-level version using directives, compare code structure, and describe barriers that were overcome in this effort.

Thavappiragasam, Mathialakan↗