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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

PANDORA: A Parallel Dendrogram Construction Algorithm for Single Linkage Clustering on GPU

This paper introduces Pandora, a parallel algorithm for computing dendrograms, the hierarchical cluster trees for single linkage clustering (SLC). Current parallel approaches construct dendrograms by partitioning a minimum spanning tree and removing edges. However, they struggle with skewed, hard-to-parallelize real-world dendrograms. Consequently, computing dendrograms is the sequential bottleneck in HDBSCAN*[21], a popular SLC variant. Pandora uses recursive tree contraction to address this limitation. Pandora contracts nodes to construct progressively smaller trees. It computes the smallest contracted dendrogram and expands it by inserting contracted edges. This recursive strategy is highly parallel, skew-independent, work-optimal, and well-suited for GPUs and multicores. We develop a performance portable implementation of Pandora in Kokkos[31] and evaluate its performance on multicore CPUs and multi-vendor GPUs (e.g., Nvidia, AMD) for dendrogram construction in HDBSCAN*. Multithreaded Pandora is 2.2x faster than the current best-multithreaded implementation. Our GPU version achieves 6-20x speedup on AMD GPUs and 10-37x on NVIDIA GPUs over multithreaded Pandora. Pandora removes HDBSCAN*’s sequential bottleneck, greatly boosting efficiency, particularly with GPUs.

Sao, Piyush↗
DOE OSTI2025

Accelerating GNNs on GPU Sparse Tensor Cores through N:M Sparsity-Oriented Graph Reordering

Recent advancements in GPU hardware support have introduced the capability to leverage N:M sparse patterns for substantial performance gains. Graphs in Graph Neural Networks (GNNs) are typically sparse, but the sparsity is often irregular, not conforming to such sparse patterns. In this paper, we propose a novel graph reordering algorithm, the first of its kind, to reshape irregular graph data into the N:M structured sparse pattern at the tile level, allowing linear-algebra-based graph operations in GNNs to benefit from the N:M sparse hardware. The optimization is lossless, maintaining the accuracy of GNN. It can remove 98-100\% violations of the N:M sparse patterns at the vector level, and increase the proportion of conforming graphs in SuiteSparse collection from 5-9\% to 88.7-93.5\%. On A100 GPUs, the optimization accelerates Sparse Matrix Matrix (SpMM) by up to 43X (2.3X -- 7.5X on average) and speeds up the key graph operations in GNNs on real graphs by as much as 8.6X (3.5X on average).

artificial intelligence, graph neural networks↗
DOE OSTI2025

NLR HPC Eagle GPU Node Metrics

Ganglia node metrics and iLO (Integrated Lights Out) power data captured from six representative Eagle GPU nodes The Eagle HPC operated at NLR from 2019 through 2024. Eagle was a 2,000-node, 8-petaflop system. This dataset is a representative sample of metrics for 6 of the GPU nodes. Each GPU node contained 2 CPUs and 2 GPUs. Data provided in compressed CSV format. Ganglia and iLO Power Time Series Fields ts: Timestamp dv: Device / Node - Rack and Unit - r103u17 == r(ack)103u(nit)17 mt: Metric (only present for Ganglia) vl: Value - Value in watts for iLO power (instantaneous value at sampling time) or specified Ganglia metric below Ganglia Metrics Metric name -- Metric description -- Unit cpu_aidle -- Percent of time since boot idle CPU -- Percent cpu_idle -- Percent CPU idle -- Percent cpu_nice -- Percent CPU nice -- Percent cpu_speed -- Speed in MHz of CPU -- MHz cpu_user -- Percent CPU user -- Percent cpu_wio -- The percentage of CPU Wait I/O -- Percent gpu0_bar1_memory -- Used GPU bar1 memory -- MB gpu0_decoder_util -- GPU decoder utilization -- Percent gpu0_ecc_db_error -- Total ECC error counts for the GPU -- Number gpu0_encoder_util -- GPU encoder utilization -- Percent gpu0_fan -- Fan speed -- RPM gpu0_fb_memory -- Used GPU framebuffer memory -- MB gpu0_graphics_clock_report -- Current clock speeds for the device -- MHz gpu0_mem_total -- Memory total -- MB gpu0_mem_util -- Memory utilization -- Percent gpu0_power_usage_report -- Power usage report -- Watts gpu0_temp -- GPU 1 temperature -- Celsius gpu1_bar1_memory -- Used GPU bar1 memory -- MB gpu1_decoder_util -- GPU decoder utilization -- Percent gpu1_ecc_db_error -- Total ECC error counts for the GPU -- Number gpu1_encoder_util -- GPU encoder utilization -- Percent gpu1_fan -- Fan speed -- RPM gpu1_fb_memory -- Used GPU framebuffer memory -- MB gpu1_graphics_clock_report -- Current clock speeds for the GPU -- MHz gpu1_mem_total -- Memory total -- MB gpu1_mem_util -- Memory utilization -- MB gpu1_power_usage_report -- Power usage report -- Watts gpu1_temp -- GPU 1 temperature -- Celsius ipmi_cpu1_temp -- CPU 1 temperature -- Celsius ipmi_cpu2_temp -- CPU 2 temperature -- Celsius ipmi_inlet_ambient_temp -- Temperature measured at intake -- Celsius ipmi_vr_p1_temp -- CPU 1 voltage regulator temperature -- Celsius ipmi_vr_p2_temp -- CPU 2 voltage regulator temperature -- Celsius mem_buffers -- Amount of buffered memory -- Bytes mem_cached -- Amount of cached memory -- Bytes mem_free -- Amount of available memory -- Bytes mem_shared -- Amount of shared memory -- Bytes mem_total -- Amount of available memory -- Bytes

97 MATHEMATICS AND COMPUTING↗
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 OSTI2024

Dual Channel Dual Staging: Hierarchical and Portable Staging for GPU-Based In-Situ Workflow

In-situ workflows have emerged as an attractive approach for addressing data movement challenges at very large scales. Since GPU-based architectures dominate the HPC landscapes, porting these in-situ workflows, and, specifically, the inter-application data exchange, to GPU-based systems can be challenging. Technologies such as GPUDirect RDMA (GDR), which is typically used for I/O in GPU applications as an optimization that circumvents the CPU overhead, can be leveraged to support bulk data exchanges between GPU applications. However, current GDR design often lacks performance portability across HPC clusters built with different hardware configurations. Furthermore, the local CPU may also be effectively used as an auxiliary communication mechanism to offload data exchanges. In this paper, we present a dual channel dual staging approach for efficient, scalable, and performance-portable inter-application data exchange for in-situ workflows. This approach exploits the data access pattern within in-situ workflows along with the inherent execution asynchrony to accelerate data exchanges and, at the same time, improve performance portability. Specifically, the dual channel dual staging method leverages both the local CPU and the remote data staging server to build a hierarchical joint staging area and uses this staging area to transform blocking inter-application bulk data exchanges into best-effort local data movements between GPU and CPU. The dual channel dual staging is implemented as a portability extension of the Dataspaces-GPU staging framework. We present an experimental evaluation of its performance, portability, and scalability using this implementation on three leadership GPU clusters. The evaluation results demonstrate that the dual channel dual staging method saves up to 75% in data-exchange time compared to host-based, GDR, and alternate portable designs, while maintaining scalability (up to 512 GPUs) and performance portability across the three platforms.

Zhang, Bo [University of Utah]↗
DOE OSTI2024

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (distributed parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

graph algorithms, high performance comptuing↗
DOE OSTI2025

A GPU Accelerated Mixed‐Precision Finite Difference Informed Random Walker (FDiRW) Solver for Strongly Inhomogeneous Diffusion Problems

In nature, many complex multi‐physics coupling problems exhibit significant diffusivity inhomogeneity, where one process occurs several orders of magnitude faster than others temporally. Simulating rapid diffusion alongside slower processes demands intensive computational resources due to the necessity for small time steps. To address these computational challenges, we have developed an efficient numerical solver named Finite Difference informed Random Walker (FDiRW). In this study, we propose a GPU‐accelerated, mixed‐precision configuration for the FDiRW solver to maximize efficiency through GPU multi‐threaded parallel computation and lower precision computation. Numerical evaluation results reveal that the proposed GPU‐accelerated mixed‐precision FDiRW solver can achieve a 117× speedup over the CPU baseline, while an additional 1.75× speedup is achieved by employing lower precision GPU computation. Notably, for large model sizes, the GPU‐accelerated mixed‐precision FDiRW solver demonstrates strong scaling with the number of nodes used in simulation. When simulating radionuclide absorption processes by porous wasteform particles with a medium‐sized model of 192 × 192 × 192, this approach reduces the total computational time to 10 min, enabling the simulation of larger systems with strongly inhomogeneous diffusivity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

A GPU-based compressible combustion solver for applications exhibiting disparate space and time scales

High-speed chemically active flows pose significant computational challenges due to their disparate space and time scales, with stiff chemistry often dominating simulation time. While modern scientific computing programs achieve exascale performance by leveraging graphics processing units (GPUs), existing GPU-based compressible combustion solvers face critical limitations in memory management, load balancing, and handling the highly localized nature of chemical reactions. To this end, we present a high-performance compressible reacting flow solver built on the AMReX framework and optimized for multi-GPU settings. Here, our approach addresses three GPU performance bottlenecks: memory access patterns through column-major storage optimization, computational workload variability via a bulk-sparse integration strategy for chemical kinetics, and multi-GPU load distribution for adaptive mesh refinement applications. The solver adapts existing matrix-based chemical kinetics formulations to multi-grid contexts. Using representative combustion applications, including 2D and 3D detonations and a 3D jet-in-crossflow configuration, we demonstrate 1.4–5× performance improvements over initial implementations on an in-house cluster of NVIDIA H100 GPUs, and near-ideal weak scaling on the Frontier supercomputer (Oak Ridge Leadership Computing Facility) with up to 1024 AMD Instinct MI250X GPUs. Roofline analysis reveals substantial improvements in arithmetic intensity for both convection (∼ 10 ×) and chemistry (∼ 4 ×) routines, confirming efficient utilization of GPU memory bandwidth and computational resources.

42 ENGINEERING↗
DOE OSTI2026

DEM Modeling and Validation of Pebble Bed Packing Using Chrono::GPU

Accurate prediction of pebble packing structure is important for pebble bed reactors because the spatial distribution of void fraction directly affects coolant flow, pressure drop, heat transfer, and neutronic behavior. However, experimentally validated DEM studies that directly evaluate local void-fraction structure in reactor-relevant pebble beds remain limited. In this work, the pebble bed experiment conducted at Missouri University of Science and Technology is simulated using the graphics processing unit (GPU)-based discrete element method (DEM) code Chrono::GPU. The study focuses on evaluating the ability of Chrono::GPU to reproduce the packing arrangement and void-fraction distribution of a randomly packed spherical pebble bed. The DEM results are first verified against established radial void-fraction correlations, including the Mueller and Vortmeyer-Schuster models, to assess the predicted bulk porosity, near-wall behavior, and oscillatory packing structure. The simulation is then verified against reference DEM data and validated against gamma-ray computed tomography (CT) experimental data at three axial locations. The Chrono::GPU results reproduce the main features of the experimental packing, including the high void fraction near the wall, the first near-wall trough, and the damped oscillatory radial profile caused by wall-induced ordering. Quantitative comparison with DEM data and the CT-based radial profiles shows good agreement, with mean absolute errors on the order of 0.07 and root-mean-square errors below 0.09 for the averaged profiles. These results demonstrate that Chrono::GPU can accurately capture the void-fraction structure of spherical pebble beds and provides a reliable DEM framework for future pebble bed reactor packing, recycling, and thermal-hydraulic studies.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Profile Generation for GPU Targets

GPU accelerators are ubiquitous, but their ecosystem is far less evolved than the host one. Compiler heuristics are often tuned for CPUs and reused for GPU. Similarly, tooling and more evolved optimization techniques are historically not available on GPU targets. In this work, we address one of these shortcomings and enable profile generation and profile-guided optimizations (PGO) for GPU targets. While this is only a single step towards a CPU equivalent ecosystem for offload devices, it shows how old misconceptions on the limitations of GPUs are often not warranted anymore. Through our implementation in LLVM/Offload, we enable device-side PGO for full scientific applications and open up tooling opportunities, including code coverage analysis and compiler-built-in roofline analysis. Our evaluation highlights the performance implications of profile generation, the insights gained from these profiles, and the (missed) opportunities in utilizing the information for GPU compilation.

McDonough, Ethan Luis [Lawrence Livermore National↗
DOE OSTI2024

VAN-DAMME: GPU-accelerated and symmetry-assisted quantum optimal control of multi-qubit systems

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated VAN-DAMME code, we carried out QOC calculations of systems containing 10 - 15 qubits, which showed that our GPU implementation is 18.4× faster than the corresponding CPU implementation. Our GPU-accelerated enhancements allow efficient calculations of multi-qubit systems, which can be used for the efficient implementation of QOC applications across multiple domains.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

LibERI—A portable and performant multi-GPU accelerated library for electron repulsion integrals via OpenMP offloading and standard language parallelism

A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.g., Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low and high contraction s, p, and d functions using the rotated-axis and Rys quadrature methods. GPU codes are factorized based on previous developments with two layers of integral screening and quartet presorting. In this work, the density screening is moved to the GPU to enhance the computational efficacy for large molecular systems. Here, the L-shells in the Pople basis set are also separated into pure S and P shells to increase the ERI homogeneity and reduce atomic operations and the memory footprint. LibERI is compatible with any quantum chemistry drivers supporting the MolSSI Driver Interface. Benchmark calculations of LibERI interfaced with the GAMESS software package were carried out on various GPU architectures and molecular systems. The results show that the LibERI performance is comparable to other state-of-the-art GPU-accelerated codes (e.g., TeraChem and GMSHPC) and, in some cases, outperforms conventionally developed ERI CUDA kernels (e.g., QUICK) while fully maintaining portability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs

Genome-wide association studies (GWAS) at biobank scale are computationally intensive, especially for admixed populations requiring robust statistical models. SAIGE is a widely used method for generalized linear mixed-model GWAS but is limited by its CPU-based implementation, making phenome-wide association studies impractical for many research groups. We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. Applied to 2068 phenotypes from 635 969 participants in the Million Veteran Program, including diverse and admixed populations, SAIGE-GPU achieved a 5-fold speedup in mixed model fitting on supercomputing infrastructure and cloud platforms. We further optimized the variant association testing step through multi-core and multi-trait parallelization. Deployed on Google Cloud Platform and Azure, the method provided substantial cost and time savings. Source code and binaries are available for download at https://github.com/saigegit/SAIGE/tree/SAIGE-GPU-1.3.3. A code snapshot is archived at Zenodo for reproducibility (DOI: [10.5281/zenodo.17642591]). SAIGE-GPU is available in a containerized format for use across HPC and cloud environments and is implemented in R/C++ and runs on Linux systems.

Rodriguez, Alex [Argonne National Laboratory (ANL)↗
DOE OSTI2025

Accelerating Neutrino Event Generation in MARLEY Using CUDA-Based RNG and GPU Parallelization

MARLEY is a simulation tool that helps scientists study how low-energy neutrinos interact with matter. To work properly, MARLEY uses random numbers thousands of times in each simulation. These random numbers are important for modeling things like how neutrinos collide with atoms and what particles they produce. Right now, MARLEY runs on a regular computer processor (CPU) and uses a built-in random number generator called the Mersenne Twister. This setup works, but it can be slow, especially when trying to simulate many events. This research focuses on making MARLEY run faster by moving the random number generation and some of the repetitive calculations from the CPU to a graphics processing unit (GPU), which can handle many tasks at the same time. We use CUDA (a tool for programming NVIDIA GPUs) and cuRAND (a GPU-based random number library) to test faster alternatives to the current random number system. We compare different GPU-based generators, like curand_mtgp32, xorwow, and philox, to see which ones are the quickest and still give reliable results. Early tests show that using the GPU can make MARLEY simulations much faster. This project not only helps improve current simulation performance but also moves closer to a full simulation chain where all stages can run on modern GPU hardware.

Dunkley, Kimieka [Florida A-M]↗
DOE OSTI2024

MAGMA: Enabling exascale performance with accelerated BLAS and LAPACK for diverse GPU architectures

MAGMA (Matrix Algebra for GPU and Multicore Architectures) is a pivotal open-source library in the landscape of GPU-enabled dense and sparse linear algebra computations. With a repertoire of approximately 750 numerical routines across four precisions, MAGMA is deeply ingrained in the DOE software stack, playing a crucial role in high-performance computing. Notable projects such as ExaConstit, HiOP, MARBL, and STRUMPACK, among others, directly harness the capabilities of MAGMA. In addition, the MAGMA development team has been acknowledged multiple times for contributing to the vendors’ numerical software stacks. Looking back over the time of the Exascale Computing Project (ECP), we highlight how MAGMA has adapted to recent changes in modern HPC systems, especially the growing gap between CPU and GPU compute capabilities, as well as the introduction of low precision arithmetic in modern GPUs. We also describe MAGMA’s direct impact on several ECP projects. Maintaining portable performance across NVIDIA and AMD GPUs, and with current efforts toward supporting Intel GPUs, MAGMA ensures its adaptability and relevance in the ever-evolving landscape of GPU architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Introducing GPU Acceleration into the Python-Based Simulations of Chemistry Framework

We introduce the first version of GPU4P Y SCF, a module that provides GPU acceleration of methods in P Y SCF. As a core functionality, this provides a GPU implementation of two-electron repulsion integrals (ERIs) for contracted basis sets comprising up to g functions using the Rys quadrature. As an illustration of how this can accelerate a quantum chemistry workflow, we describe how to use the ERIs efficiently in the integral-direct Hartree–Fock build and nuclear gradient construction. Benchmark calculations show a significant speedup of 2 orders of magnitude with respect to the multithreaded CPU Hartree–Fock code of P Y SCF and the performance comparable to other open-source GPU-accelerated quantum chemical packages, including GAMESS and QUICK, on a single NVIDIA A100 GPU.

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

Beyond the Bridge: Contention-Based Covert and Side Channel Attacks on Multi-GPU Interconnect

Recently, high-speed interconnects like NVLink have become a standard integration in modern multi-GPU systems, serving as a crucial bridge between CPUs and GPUs. This study highlights the vulnerability of multi-GPU systems to covert and side-channel attacks arising from congestion on these interconnects. An adversary, operating without special permissions, can extract private information about a victim's activities by monitoring NVLink congestion. Specifically, we leverage this insight to develop a covert channel attack across two GPUs, achieving a respectable bandwidth of 33 Kbps. Additionally, we introduce a side-channel attack that allows attackers to fingerprint applications on a remote GPU by probing the shared NVLink interconnect. We underscore the urgent nature of the threats posed by these attacks and advocate for heightened awareness within both industry and academia to implement multi-GPU interconnects with enhanced security measures.

Zhang, Yicheng↗
DOE OSTI2026

Wattchmen: Watching the Wattchers – High Fidelity, Flexible GPU Energy Modeling

Modern GPU-rich HPC systems are increasingly becoming energy-constrained. Thus, understanding an application’s energy consumption becomes essential. Unfortunately, current GPU energy attribution techniques are either inaccurate, inflexible, or outdated. Therefore, we propose Wattchmen, a flexible methodology for measuring, attributing, and predicting GPU energy consumption. We construct a per-instruction energy model using a diverse set of microbenchmarks to systematically quantify the energy consumption of GPU instructions, enabling finer-grain prediction and energy consumption breakdowns for applications. Compared with the state-of-the-art systems like AccelWattch (32%) and Guser (25%), across 16 popular GPGPU, graph analytics, HPC, and ML workloads, Wattchmen reduces the mean absolute percent error (MAPE) to 14% on V100 GPUs. Furthermore, we show that Wattchmen provides similar MAPEs for water-cooled V100s (15%) and extends to later architectures, including air-cooled A100 (11%) and H100 (12%) GPUs. Finally, to further demonstrate Wattchmen ’s value, we apply it to applications such as Backprop and QMCPACK, where Wattchmen ’s insights enable energy reductions of up to 35%.

Tran, Brandon [University of Wisconsin, Madison] (↗