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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Accelerating x-ray tracing for exascale systems using Kokkos

The upcoming exascale computing systems Frontier and Aurora will draw much of their computing power from GPU accelerators. The hardware for these systems will be provided by AMD and Intel, respectively, each supporting their own GPU programming model. The challenge for applications that harness one of these exascale systems will be to avoid lock-in and to preserve performance portability. We report here on our results of using Kokkos to accelerate a real-world application on NERSC's Perlmutter Phase 1 (using NVIDIA A100 accelerators) and Crusher, the testbed system for OLCF's Frontier (using AMD MI250X). By porting to Kokkos, we successfully ran the same X-ray tracing code on both systems and achieved speed-ups between 13 % and 66 % compared to the original CUDA code. Finally, these results are a highly encouraging demonstration of using Kokkos to accelerate production science code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

h5bench: A unified benchmark suite for evaluating HDF5 I/O performance on pre‐exascale platforms

Summary Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Bringing HPE Slingshot 11 support to Open MPI

The Cray HPE Slingshot 11 network is used on the new exascale systems arriving at the U.S. Department of Energy (DoE) laboratories (e.g., Frontier, Aurora, Perlmutter). As such, the support of this network is an important capability to meet the needs of exascale applications. Here, this article highlights recent work to develop supporting infrastructure to enable Open MPI to efficiently support these new platforms. A key component of this effort involves development of a new Open Fabrics Interface (OFI) provider, LinkX. We discuss the design and development of enhancements that take advantage of the new Slingshot 11 network and AMD GPUs. We include performance data from tests on the Frontier supercomputer using synthetic communication benchmarks, and the vendor provided MPI as a baseline for comparison. The tests demonstrate full functionality of Open MPI on the system and initial results show favorable performance when compared to the highly tuned vendor implementation.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2026

Multi-task Parallelism for Robust Pre-training of Graph Foundation Models on Multi-source, Multi-fidelity Atomistic Modeling Data

Graph foundation models using graph neural networks promise sustainable, efficient atomistic modeling. To tackle challenges of processing multi-source, multi-fidelity data during pre-training, recent studies employ multi-task learning, in which shared message passing layers initially process input atomistic structures regardless of source, then route them to multiple decoding heads that predict data-specific outputs. This approach stabilizes pre-training and enhances a model’s transferability to unexplored chemical regions. Preliminary results on approximately four million structures are encouraging, yet questions remain about generalizability to larger, more diverse datasets and scalability on supercomputers. We propose a multi-task parallelism method that distributes each head across computing resources with GPU acceleration. Implemented in the open-source HydraGNN architecture, our method was trained on over 24 million structures from five datasets and tested on the Perlmutter, Aurora, and Frontier supercomputers, demonstrating efficient scaling on all three highly heterogeneous super-computing architectures.

Lupo Pasini, Massimiliano [ORNL] (ORCID:0000000249↗
DOE OSTI2023

Model-parallel Fourier neural operators as learned surrogates for large-scale parametric PDEs

Fourier neural operators (FNOs) are a recently introduced neural network architecture for learning solution operators of partial differential equations (PDEs), which have been shown to perform significantly better than comparable deep learning approaches. Once trained, FNOs can achieve speed-ups of multiple orders of magnitude over conventional numerical PDE solvers. However, due to the high dimensionality of their input data and network weights, FNOs have so far only been applied to two-dimensional or small three-dimensional problems. To remove this limited problem-size barrier, we propose a model-parallel version of FNOs based on domain-decomposition of both the input data and network weights. Here, we demonstrate that our model-parallel FNO is able to predict time-varying PDE solutions of over 2.6 billion variables on Perlmutter using up to 512 A100 GPUs and show an example of training a distributed FNO on the Azure cloud for simulating multiphase CO 2 dynamics in the Earth’s subsurface.

58 GEOSCIENCES↗
DOE OSTI2025

Acceleration of the particle-in-cell code Osiris with graphics processing units

Fully relativistic particle-in-cell (PIC) simulations are crucial for advancing our knowledge of plasma physics. Modern supercomputers based on graphics processing units (GPUs) offer the potential to perform PIC simulations of unprecedented scale, but require robust and feature-rich codes that can fully leverage their computational resources. In this work, this demand is addressed by adding GPU acceleration to the PIC code Osiris. An overview of the algorithm, which features a CUDA extension to the underlying Fortran architecture, is given. Detailed performance benchmarks for thermal plasmas are presented, which demonstrate excellent weak scaling on NERSC's Perlmutter supercomputer and high levels of absolute performance. The robustness of the code to model a variety of physical systems is demonstrated via simulations of Weibel filamentation and laser-wakefield acceleration run with dynamic load balancing. Finally, measurements and analysis of energy consumption are provided that indicate that the GPU algorithm is up to ~14 times faster and ~7 times more energy efficient than the optimized CPU algorithm on a node-to-node basis. The described development addresses the PIC simulation community's computational demands both by contributing a robust and performant GPU-accelerated PIC code and by providing insight into efficient use of GPU hardware.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Distributed memory, GPU accelerated Fock construction for hybrid, Gaussian basis density functional theory

With the growing reliance of modern supercomputers on accelerator-based architecture such a graphics processing units (GPUs), the development and optimization of electronic structure methods to exploit these massively parallel resources has become a recent priority. While significant strides have been made in the development GPU accelerated, distributed memory algorithms for many modern electronic structure methods, the primary focus of GPU development for Gaussian basis atomic orbital methods has been for shared memory systems with only a handful of examples pursing massive parallelism. Here in this work, we present a set of distributed memory algorithms for the evaluation of the Coulomb and exact exchange matrices for hybrid Kohn–Sham DFT with Gaussian basis sets via direct density-fitted (DF-J-Engine) and seminumerical (sn-K) methods, respectively. The absolute performance and strong scalability of the developed methods are demonstrated on systems ranging from a few hundred to over one thousand atoms using up to 128 NVIDIA A100 GPUs on the Perlmutter supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Accelerated kinetic model for global macro stability studies of high-beta fusion reactors

The field reversed configuration (FRC), such as studied in the C-2W experiment at TAE Technologies, is an attractive candidate for realizing a nuclear fusion reactor. In an FRC, kinetic ion effects play the majority role in macroscopic stability, which allows global stability studies to make use of fluid-kinetic hybrid (also referred to as Ohm's law) models wherein ions are treated kinetically while electrons are treated as a fluid. The development and validation of such a hybrid particle-in-cell algorithm in the Exascale Computing Project code WarpX are reported here. Implementation of this model in the WarpX framework benefits from the numerical efficiency of WarpX as well as its scalability on large HPC systems and portability to different architectures. Performance benchmarks of the new algorithm for large, 3-dimensional, full device simulations from the Perlmutter supercomputer are presented. Results of a series of FRC simulations are discussed in which the impact of two-fluid effects on the tilt-mode growth rate was studied. It was observed that, in agreement with previous Hall-MHD studies, two-fluid effects have a stabilizing impact on the tilt mode.

Physics↗
DOE OSTI2026

pyRMG: A framework for high-throughput, large-cell DFT calculations on supercomputers

Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density functional theory (DFT) code’s grid-decomposition approach scales nearly linearly with the number of graphics processing units (GPUs), even for simulations exceeding thousands of atoms. This scalability makes RMG a compelling tool for high-throughput DFT studies of materials that would otherwise be bottlenecked in other codes (for example, by global fast Fourier transforms in plane-wave DFT). However, the limited workflow infrastructure for RMG has thus far constrained its adoption to a small user community. In this work, we present pyRMG, a Python package designed to streamline the setup and execution of RMG DFT calculations. Built on the pymatgen and ASE (Atomic Simulation Environment) computational materials science Python packages, pyRMG automates input generation and convergence checking, and it integrates with modern job schedulers (e.g., Flux) on leadership-class platforms such as Frontier and Perlmutter. Here, we demonstrate pyRMG for a high-throughput study of strain effects in 2D 2L-Bi 2 Se 3 /2L-NbSe 2 heterostructures, which offers chemical insights into this system and shows that RMG-based workflows can converge with limited user intervention.

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

MassiveGNN: Efficient Training via Prefetching for Massively Connected Distributed Graphs

Graph Neural Networks (GNN) are indispensable in learning from graph-structured data, yet their rising computational costs, especially on massively connected graphs, pose significant challenges in terms of execution performance. To tackle this, distributed-memory solutions such as partitioning the graph to concurrently train multiple replicas of GNNs are in practice. However, approaches requiring a partitioned graph usually suffer from communication overhead and load imbalance, even under optimal partitioning and communication strategies due to irregularities in the neighborhood minibatch sampling. This paper proposes practical trade-offs for improving the sampling and communication overheads for representation learn- ing on distributed graphs (using popular GraphSAGE architecture) by developing a parameterized prefetch and eviction scheme on top of the state-of-the-art Amazon DistDGL distributed GNN framework, demonstrating about 15–40% improvement in end-to-end training performance on the NERSC Perlmutter supercomputer for various OGB datasets.

Machine Leanring, high performance comptuing, grap↗
DOE OSTI2024

Optimizing the Weather Research and Forecasting Model with OpenMP Offload and Codee

Currently, the Weather Research and Forecasting model (WRF) utilizes shared memory (OpenMP) and distributed memory (MPI) parallelisms. To take advantage of GPU resources on the Perlmutter supercomputer at NERSC, we port parts of the computationally expensive routine Fast Spectral Bin Microphysics (FSBM) to NVIDIA GPUs using OpenMP device offloading directives. To facilitate this process, we explore a workflow for optimization which uses both runtime profilers and a static code inspection tool Codee to refactor the subroutine. We observe an 2.24x overall speedup for the CONUS-12km storm test case.

Wichitrnithed, Chayanon (Namo) [Odin Institute]↗
DOE OSTI2024

Enabling Low-Overhead HT-HPC Workflows at Extreme Scale using GNU Parallel

GNU Parallel is a versatile and powerful tool for process parallelization widely used in scientific computing. This paper demonstrates its effective application in high-performance computing (HPC) environments, particularly focusing on its scalability and efficiency in executing large-scale high-throughput high-performance computing (HT-HPC) workflows. Through real-world examples, we highlight GNU Parallel’s performance across various HPC workloads, including GPU computing, container-based workloads, and node-local NVMe storage. Our results on two leading supercomputers, OLCF’s Frontier and NERSC’s Perlmutter, showcase GNU Parallel’s rapid process dispatching ability and its capacity to maintain low overhead even at extreme scales. We explore GNU Parallel’s application in massive parallel file transfers using a scheduled Data Transfer Node (DTN) cluster, emphasizing its broad utility in diverse scientific workflows. Beyond its direct application as a viable workflow manager, GNU Parallel can be employed in conjunction with other workflow systems as a "last-mile" parallelizing driver and as a quick prototyping tool to design and extract parallel profiles from application executions. We then argue that the potential for GNU Parallel to transform workflow management at extreme scales is substantial, paving the way for more efficient and effective scientific discoveries.

Maheshwari, Ketan↗
DOE OSTI2023

Unified Communication Optimization Strategies for Sparse Triangular Solver on CPU and GPU Clusters

This paper presents a unified communication optimization framework for sparse triangular solve (SpTRSV) algorithms on CPU and GPU clusters. The framework builds upon a 3D communication-avoiding (CA) layout of Px × Py × Pz processes that divides a sparse matrix into Pz submatrices, each handled by a Px × Py 2D grid with block-cyclic distribution. We propose three communication optimization strategies: First, a new 3D SpTRSV algorithm is developed, which trades the inter-grid communication and synchronization with replicated computation. This design requires only one inter-grid synchronization, and the inter-grid communication is efficiently implemented with sparse allreduce operations. Second, broadcast and reduction communication trees are used to reduce message latency of the intra-grid 2D communication on CPU clusters. Finally, we leverage GPU-initiated one-sided communication to implement the communication trees on GPU clusters. With these nested inter- and intra-grid communication optimization strategies, the proposed 3D SpTRSV algorithm can attain up to 3.45x speedups compared to the baseline 3D SpTRSV algorithm using up to 2048 Cori Haswell CPU cores. In addition, the proposed GPU 3D SpTRSV algorithm can achieve up to 6.5x speedups compared to the proposed CPU 3D SpTRSV algorithm with Pz up to 64. Finally it is remarkable that the proposed GPU 3D SpTRSV can scale to 256 GPUs using the Perlmutter system while the existing 2D SpTRSV algorithm can only scale up to 4 GPUs.

Sao, Piyush↗
DOE OSTI2023

DDStore: Distributed Data Store for Scalable Training of Graph Neural Networks on Large Atomistic Modeling Datasets

Graph neural networks (GNNs) are a class of Deep Learning models used in designing atomistic materials for effective screening of large chemical spaces. To ensure robust prediction, GNN models must be trained on large volumes of atomistic data on leadership class supercomputers. Even with the advent of modern architectures that consist of multiple storage layers that include node-local NVMe devices in addition to device memory for caching large datasets, extreme-scale model training faces I/O challenges at scale.We present DDStore, an in-memory distributed data store designed for GNN training on large-scale graph data. DDStore provides a hierarchical, distributed, data caching technique that combines data chunking, replication, low-latency random access, and high throughput communication. DDStore achieves near-linear scaling for training a GNN model using up to 1000 GPUs on the Summit and Perlmutter supercomputers, and reaches up to a 6.15x reduction in GNN training time compared to state-of-the-art methodologies.

Choi, Jong Youl↗
DOE OSTI2023

Performance-Portable GPU Acceleration of the EFIT Tokamak Plasma Equilibrium Reconstruction Code

This paper presents the steps followed to GPU-offload parts of the core solver of EFIT-AI, an equilibrium reconstruction code suitable for tokamak experiments and burning plasmas. For this work, we will focus on the fitting procedure that consists of a Grad–Shafranov (GS) equation inverse solver that calculates equilibrium reconstructions on a grid. We will show profiling results of the original code (CPU-baseline), as well as the directives used to GPU-offload the most time-consuming function, initially to compare OpenACC and OpenMP on NVIDIA and AMD GPUs and later on to assess OpenMP performance portability on NVIDIA, AMD and Intel GPUs. We will make a performance comparison for different spatial grid sizes and show the speedup achieved on NVIDIA A100 (Perlmutter-NERSC), AMD MI250X (Frontier-OLCF) and Intel PVC GPUs (Sunspot-ALCF). Finally, we will draw some conclusions and recommendations to achieve high-performance portability for an equilibrium reconstruction code on the new HPC architectures

GPU↗
DOE OSTI2023

HydraGNN 2.0

HydraGNN is an Oak Ridge National Laboratory (ORNL)-branded implementation of distributed multi-tasking graph neural networks that supports several scientific applications within the ORNL portfolio to support the US-DOE mission. New or improved capabilities included in v2.0.0 release are as follows: 1) Enhancement in message passing layers through class inheritance 2) Adding transformation to ensure translation and rotation invariance 3) Supporting various optimizers 4) Atomic descriptors 5) Integration with continuous CI test 6) Distributed printouts and timers 7) Profiling 8) Support of ADIOS2 for scalable data loading 9) Large-scale system support, including Summit (ORNL) and Perlmutter (NERSC)

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗