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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Direct numerical simulations of turbulent reacting flows with shock waves and stiff chemistry using many-core/GPU acceleration

Compressible reacting flows may display sharp spatial variation related to shocks, contact discontinuities or reactive zones embedded within relatively smooth regions. The presence of such phenomena emphasizes the relevance of shock-capturing schemes such as the weighted essentially non-oscillatory (WENO) scheme as an essential ingredient of the numerical solver. However, these schemes are complex and have more computational cost than the simple high-order compact or non-compact schemes. In this paper, we present the implementation of a seventh-order, minimally-dissipative mapped WENO (WENO7M) scheme in a newly developed direct numerical simulation (DNS) code called KAUST Adaptive Reactive Flows Solver (KARFS). In order to make efficient use of the computer resources and reduce the solution time, without compromising the resolution requirement, the WENO routines are accelerated via graphics processing unit (GPU) computation. The performance characteristics and scalability of the code are studied using different grid sizes and block decomposition. Furthermore, the performance portability of KARFS is demonstrated on a variety of architectures including NVIDIA Tesla P100 GPUs and NVIDIA Kepler K20X GPUs. In addition, the capability and potential of the newly implemented WENO7M scheme in KARFS to perform DNS of compressible flows is also demonstrated with model problems involving shocks, isotropic turbulence, detonations and flame propagation into a stratified mixture with complex chemical kinetics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

GPU-acceleration of the ELPA2 distributed eigensolver for dense symmetric and hermitian eigenproblems

The solution of eigenproblems is often a key computational bottleneck that limits the tractable system size of numerical algorithms, among them electronic structure theory in chemistry and in condensed matter physics. Large eigenproblems can easily exceed the capacity of a single compute node, thus must be solved on distributed-memory parallel computers. We here present GPU-oriented optimizations of the ELPA two-stage tridiagonalization eigensolver (ELPA2). On top of cuBLAS-based GPU offloading, we add a CUDA kernel to speed up the back-transformation of eigenvectors, which can be the computationally most expensive part of the two-stage tridiagonalization algorithm. Furthermore, we benchmark the performance of this GPU-accelerated eigensolver on two hybrid CPU–GPU architectures, namely a compute cluster based on Intel Xeon Gold CPUs and NVIDIA Volta GPUs, and the Summit supercomputer based on IBM POWER9 CPUs and NVIDIA Volta GPUs. Consistent with previous benchmarks on CPU-only architectures, the GPU-accelerated two-stage solver exhibits a parallel performance superior to the one-stage counterpart. Finally, we demonstrate the performance of the GPU-accelerated eigensolver developed in this work for routine semi-local KS-DFT calculations comprising thousands of atoms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Record acceleration of the two-dimensional Ising model using a high-performance wafer-scale engine

The versatility and wide-ranging applicability of the Ising model, originally introduced to study phase transitions in magnetic materials, have made it a cornerstone in statistical physics and a valuable tool for evaluating the performance of emerging computer hardware. Here, we present a novel implementation of the two-dimensional Ising model on Cerebras Wafer-Scale Engine (WSE) – a revolutionary processor that is opening new frontiers in computing. In our deployment of the checkerboard algorithm, we optimized the Ising model to take advantage of the unique WSE architecture. Specifically, we employed a compressed bit representation storing 16 spins on each int16 word, and efficiently distributed the spins over the processing units enabling seamless weak scaling and limiting communications to only immediate neighboring units. Our implementation can handle up to 754 simulations in parallel, achieving an aggregate of over 61.8 trillion flip attempts per second for Ising models with up to 200 million spins. This represents a gain of up to 148 times over previously reported single-devices with a highly optimized implementation on NVIDIA V100 and up to 88 times in productivity compared to NVIDIA H100. Our findings highlight the significant potential of the WSE in scientific computing, particularly in the field of materials modeling.

Ising model↗
DOE OSTI2022

Towards scaling community detection on distributed-memory heterogeneous systems

Distributed multi-GPU systems pose significant challenges and opportunities for efficient execution of parallel applications. Graph algorithms are generally characterized by irregular memory accesses, low computation to communication ratios, and load balancing problems that are especially hard to address on multi-GPU systems. Graph community detection is an important problem in the emerging domain of graph analytics with numerous applications. In this paper, we present our ongoing work on distributed-memory multi-GPU implementation for graph community detection. Our work parallelizes the widely used (albeit serial) Louvain method on distributed multi-GPU platforms. Supported by an extensive set of experiments on a multi-GPU enabled supercomputer (OLCF Summit) and a single compute node (Nvidia DGX-2®), we demonstrate competitive performance to existing distributed-memory CPU-based implementation, and up to 6.5 better results than Nvidia RAPIDS® CUGRAPH. To the best of our knowledge, this work represents the first effort for community detection on distributed multi-GPU systems. Our approach and related findings can be extended to numerous other iterative graph algorithms on multi-GPU systems.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2020

Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction

In this study, we have extended our graphical processing unit (GPU)-accelerated direct configuration interaction program to multiple devices, reducing iteration times for configuration spaces of 165 million determinants to only 3 s using NVIDIA P100 GPUs. Similar improvements in the one- and two-particle reduced density matrix formation allow for fast analytical energy gradients and electronic properties. Our parallel algorithm enables the calculation of arbitrarily large configuration spaces (limited only by available system memory), with iteration times of 13 min for an active space of 18 electrons in 18 orbitals (2.4 billion determinants) using six consumer grade NVIDIA 1080Ti GPUs. These advances enable routine molecular dynamics simulations, geometry optimizations, and absorption spectrum calculations for molecules with large configuration spaces, a task that has heretofore required massive computational effort. In this work, we demonstrate the utility of our program by generating the absorption spectrum for diphenyl acetylene at the floating occupation molecular orbital complete active space configuration interaction level of theory. Lastly, several active spaces were investigated to assess the dependence of spectral features on orbital space dimension.

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

Evaluation of Portable Acceleration Solutions for LArTPC Simulation Using Wire-Cell Toolkit

The Liquid Argon Time Projection Chamber (LArTPC) technology plays an essential role in many current and future neutrino experiments. Accurate and fast simulation is critical to developing efficient analysis algorithms and precise physics model projections. The speed of simulation becomes more important as Deep Learning algorithms are getting more widely used in LArTPC analysis and their training requires a large simulated dataset. Heterogeneous computing is an efficient way to delegate computationally intensive tasks to specialized hardware. However, as the landscape of compute accelerators quickly evolves, it becomes increasingly difficult to manually adapt the code to the latest hardware or software environments. A solution which is portable to multiple hardware architectures without substantially compromising performance would thus be very beneficial, especially for long-term projects such as the LArTPC simulations. In search of a portable, scalable and maintainable software solution for LArTPC simulations, we have started to explore high-level portable programming frameworks that support several hardware backends. In this paper, we present our experience porting the LArTPC simulation code in the Wire-Cell Toolkit to NVIDIA GPUs, first with the CUDA programming model and then with a portable library called Kokkos. Preliminary performance results on NVIDIA V100 GPUs and multi-core CPUs are presented, followed by a discussion of the factors affiecting the performance and plans for future improvements.

Yu, Haiwang↗
DOE OSTI2024

Celeritas: Accelerating Geant4 with GPUs

Celeritas [1] is a new Monte Carlo (MC) detector simulation code designed for computationally intensive applications (specifically, High Lumi- nosity Large Hadron Collider (HL-LHC) simulation) on high-performance heterogeneous architectures. In the past two years Celeritas has advanced from prototyping a GPU-based single physics model in infinite medium to implementing a full set of electromagnetic (EM) physics processes in complex geometries. The current release of Celeritas, version 0.3, has incorporated full device-based navigation, an event loop in the presence of magnetic fields, and detector hit scoring. New functionality incorporates a scheduler to offload electromagnetic physics to the GPU within a Geant4-driven simulation, enabling integration of Celeritas into high energy physics (HEP) experimental frameworks such as CMSSW. On the Summit supercomputer, Celeritas performs EM physics between 6 and 32 faster using the machine’s Nvidia GPUs compared to using only CPUs. When running a multithreaded Geant4 ATLAS test beam application with full hadronic physics, using Celeritas to accelerate the EM physics results in an overall simulation speedup of 1.8–2.3× on GPU and 1.2× on CPU.

Johnson, Seth R.↗
DOE OSTI2023

Accelerating the density-functional tight-binding method using graphical processing units

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Herein two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1–6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1–2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Mixed-precision iterative refinement using tensor cores on GPUs to accelerate solution of linear systems

Double-precision floating-point arithmetic (FP64) has been the de facto standard for engineering and scientific simulations for several decades. Problem complexity and the sheer volume of data coming from various instruments and sensors motivate researchers to mix and match various approaches to optimize compute resources, including different levels of floating-point precision. In recent years, machine learning has motivated hardware support for half-precision floating-point arithmetic. A primary challenge in high-performance computing is to leverage reduced-precision and mixed-precision hardware. We show how the FP16/FP32 Tensor Cores on NVIDIA GPUs can be exploited to accelerate the solution of linear systems of equations Ax = b without sacrificing numerical stability. The techniques we employ include multiprecision LU factorization, the preconditioned generalized minimal residual algorithm (GMRES), and scaling and auto-adaptive rounding to avoid overflow. We also show how to efficiently handle systems with multiple right-hand sides. On the NVIDIA Quadro GV100 (Volta) GPU, we achieve a 4×-5× performance increase and 5× better energy efficiency versus the standard FP64 implementation while maintaining an FP64 level of numerical stability.

GMRES↗
DOE OSTI2022

Interpretable AI forecasting for numerical relativity waveforms of quasicircular, spinning, nonprecessing binary black hole mergers

We present a deep-learning artificial intelligence model (AI) that is capable of learning and forecasting the late-inspiral, merger and ringdown of numerical relativity waveforms that describe quasicircular, spinning, nonprecessing binary black hole mergers. We used the NRHybSur3dq8 surrogate model to produce train, validation and test sets of ℓ = |m| = 2 waveforms that cover the parameter space of binary black hole mergers with mass ratios q ≤ 8 and individual spins |s$^{z}_ {(1,2)}$| ≤ 0.8. These waveforms cover the time range t ∊ [-5000 M, 130 M], where t = 0M marks the merger event, defined as the maximum value of the waveform amplitude. We harnessed the ThetaGPU supercomputer at the Argonne Leadership Computing Facility to train our AI model using a training set of 1.5 million waveforms. We used 16 NVIDIA DGX A100 nodes, each consisting of 8 NVIDIA A100 Tensor Core GPUs and 2 AMD Rome CPUs, to fully train our model within 3.5 h. Our findings show that artificial intelligence can accurately forecast the dynamical evolution of numerical relativity waveforms in the time range t ∊ [-100 M, 130 M]. Sampling a test set of 190,000 waveforms, we find that the average overlap between target and predicted waveforms is ≳99% over the entire parameter space under consideration. We also combined scientific visualization and accelerated computing to identify what components of our model take in knowledge from the early and late-time waveform evolution to accurately forecast the latter part of numerical relativity waveforms. This work aims to accelerate the creation of scalable, computationally efficient and interpretable artificial intelligence models for gravitational wave astrophysics

79 ASTRONOMY AND ASTROPHYSICS↗
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↗
DOE OSTI2025

Enabling Scientific Applications with Performance-Portability and High-Productivity for Multi-GPU Programming with JACC.Multi

This work bridges the gap between multi-GPU computing and high-productivity, performance-portable programming solutions. Our goal is to enhance scientific applications with a productive and portable solution—program once, deploy everywhere—for multi-GPU programming with no cost to programmability. To accomplish this, we implemented JACC.Multi, which is part of the Julia for ACCelerators (JACC) performance-portable framework. JACC. Multi is the only high-level, portable metaprogramming solution that targets multi-GPU environments and is integrated in a readily accessible programming language (e.g., Julia language). With transparent GPU-to-GPU communication, JACC. Multi is optimized for scientific application workloads and is portable for NVIDIA and AMD accelerators. For the evaluation, we use two modern multi-GPU systems: Hudson, which features two NVIDIA H100 Hopper GPUs per node, and Frontier, which features four AMD MI250X GPUs per node, each with two Graphics Compute Dies (GCDs) for a total of eight GCDs per node. Additionally, as part of the evaluation, we use JACC (one GPU), MPI+JACC, and JACC. Multi codes that implement well-known and widely used scientific algorithms/kernels such as the conjugate gradient algorithm and an explicit forward Euler solver that requires GPU-to-GPU communication. Overall, JACC. Multi codes achieve better performance than MPI+JACC codes and significant speedups over JACC (one GPU), with up to 1.9× on Hudson and 6× on Frontier.

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗
DOE OSTI2025

JACC.shared: Leveraging HPC Metaprogramming and Performance Portability for Computations That Use Shared Memory GPUs

In this work, we present JACC.shared, a new feature of Julia for ACCelerators (JACC), which is the performanceportable and metaprogramming model of the just-in-time and LLVM-based Julia language. This new feature allows JACC applications to leverage the high-performance computing (HPC) capabilities of high-bandwidth, on-chip GPU memory. Historically, exploiting high-bandwidth, shared-memory GPUs has not been a priority for high-level programming solutions. JACC.shared covers that gap for the first time, thereby providing a highlevel, portable, and easy-to-use solution for programmers to exploit this memory and supporting all current major accelerator architectures. Well-known HPC and AI workloads, such as multi/hyperspectral imaging and AI convolutions, have been used to evaluate JACC.shared on two exascale GPU architectures hosted by some of the most powerful US Department of Energy supercomputers: Perlmutter (NVIDIA A100) and Frontier (AMD MI250X). The performance evaluation reports speedup of up to 3.5× by adding only one line of code to the base codes, thus providing important accelerators in a simple, portable, and transparent way and elevating the programming productivity and performance-portability capabilities for Julia/JACC HPC, AI, and scientific applications.

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗
DOE OSTI2023

Machine Learning Models for Network Traffic Classification in Programmable Logic

Network traffic classification via machine learning on network packet payloads has emerged as an active area of research for network security due to the high accuracy machine learning models have achieved in classifying payloads. For effective deployment as part of network security, these machine learning models must not only classify malicious packet payloads accurately, they must also identify anomalous payloads and perform inference at speeds generally faster than 10,000 packets per second to be effective. This work explores the in- ference speeds and accuracy of several neural network models implemented in programmable logic on various field programmable gate arrays (FPGA) including the Xilinx VC1902 and Xilinx Zynq Ultrascale+. This work also presents the design and performance of both an autoencoder and variational autoencoder programmed on the FPGA for identifying anomalous packet payloads. The performance benefits of the FPGA implementation for this type of packet payload inspection driven by machine learning are compared against graphics processing unit (GPU) inference implementations run on two state-of-the-art datacenter GPU devices, the NVIDIA V100 and A100. The model accuracy difference between the FPGA and GPU implementations was found to be 4% or less while the Xilinx VC1902 outperformed both the NVIDIA V100 and A100 for inference speeds on all the models explored except the variational autoencoder.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗