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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Characterization and Optimization of the Fitting of Quantum Correlation Functions

This case study presents a characterization and optimization of an application code for extracting parton distribution functions from high energy electron-proton scattering data. Profiling this application code reveals that the phase-space density computation accounts for 93% of the overall execution time for a single iteration on a single core. When executing multiple iterations in parallel on a multicore system, the application spends 78% of its overall execution time idling due to load imbalance. We address these issues by first transforming the application code from Python to C++ and then tackling the application load imbalance via a hybrid scheduling strategy that combines dynamic and static scheduling. These techniques result in a 62% reduction in CPU idle time and a 2.46x speedup in overall execution time per node. In addition, the typically enabled power-management mechanisms in supercomputers (e.g., AMD Turbo Core, Intel Turbo Boost, and RAPL) can significantly impact intra-node scalability when more than 50% of the CPU cores are used. This finding underscores the importance of understanding system interactions with power management, as they can adversely impact application performance, and highlights the necessity of intra-node scaling tests to identify performance degradation that inter-node scaling tests might otherwise overlook.

Chuang, Pi-Yueh [Virginia Tech,Dept. of Computer S↗
DOE OSTI2024

Power Profile Monitoring and Tracking Evolution of System-Wide HPC Workloads

The power & energy demands of HPC machines have grown significantly. Modern exascale HPC systems require tens of megawatts of combined power for computing resources and cooling facilities at full capacity. The current energy trend is not sustainable for future HPC systems, and there is a need to work toward the energy efficiency aspect of HPC performance. Energy awareness of the HPC applications at the job level is essential for running an efficient HPC system. This work aims to develop a pipeline to provide a production-level system-wide overview of the HPC workloads' power profile while handling evolving workloads exhibiting new power trends. We developed an open-set classification model for HPC jobs based on the properties of power profiles to continuously provide a system-wide holistic view of recently completed jobs. The pipeline helps continuously monitor the job-level power usage pattern of HPC and enables us to capture the new trends in applications' power behavior. We employed a comprehensive set of techniques to generate job-level data, custom-designed feature extraction methods to extract critical features from jobs' power profiles, clustering techniques powered by generative modeling, and open-set classification for identifying job profiles into known classes or an unknown set. With extensive evaluations, we demonstrate the effectiveness of each component in our pipeline. We provide an analysis of the resulting clusters that characterize the power profile landscape of the Summit supercomputer from more than 60K jobs executed in a year. The open-set classification classifies the known data sets into known classes with high accuracy and identifies unknown data noints with over 85% accuracy.

Karimi, Ahmad Maroof↗
DOE OSTI2021

Optimizing Error-Bounded Lossy Compression for Scientific Data by Dynamic Spline Interpolation

Today's scientific simulations are producing vast volumes of data that cannot be stored and transferred efficiently because of limited storage capacity, parallel I/O bandwidth, and network bandwidth. The situation is getting worse over time because of the ever-increasing gap between relatively slow data transfer speed and fast-growing computation power in modern supercomputers. Error-bounded lossy compression is becoming one of the most critical techniques for resolving the big scientific data issue, in that it can significantly reduce the scientific data volume while guaranteeing that the reconstructed data is valid for users because of its compression-error-bounding feature. In this paper, we present a novel error-bounded lossy compressor based on a state-of-the-art prediction-based compression framework. Our solution exhibits substantially better compression quality than all of the existing error-bounded lossy compressors, with comparable compression speed. Specifically, our contribution is threefold. (1) We provide an in-depth analysis of why the best-existing prediction-based lossy compressor can only minimally improve the compression quality. (2) We propose a dynamic spline interpolation approach with a series of optimization strategies that can significantly improve the data prediction accuracy, substantially improving the compression quality in turn. (3) We perform a thorough evaluation using six real-world scientific simulation datasets across different science domains to evaluate our solution vs. all other related works. Experiments show that the compression ratio of our solution is higher than that of the second-best lossy compressor by 20%similar to 460% with the same error bound in most of the cases.

Zhao, Kai↗
DOE OSTI2026

A Brief Survey of Data Streaming Technologies

Streaming data is data that is emitted at variable volumes in a continuous, incremental manner with the goal of low-latency processing often at a different physical location. Network infrastructure is used to facilitate the connection between data sources and sinks, and must be robust to handle the requirements of the workflow. The U.S. Department of Energy Office of Science (DOE SC) a federal agency supporting fundamental scientific research for energy and the Nation’s largest supporter of basic research in the physical sciences. DOE SC has the responsibility for operating $\mathbf{1 0}$ National Laboratories, and 28 scientific user facilities supporting advanced supercomputers, particle accelerators, large x-ray light sources, neutron scattering sources, and other specialized facilities for nanoscience and genomics. This paper investigates the state of streaming data workfows, and details some of the approaches to this challenging problem.

Kissel, Ezra↗
DOE OSTI2023

Scaling Automatic Vector Data Alignment to Satellite Imagery

Given the tremendous volume of accessible Earth Observation (EO) data, there is a need to develop scalable Geospatial Artificial Intelligence (GeoAI) solutions for time-sensitive applications. Scalability in this context refers to rapidly processing large-scale EO data using high performance computing resources. Accurate mapping of the built environment from remote sensing (RS) imagery has been one of the crucial components in GeoAI workflows for a wide spectrum of humanitarian applications. Derived vector data of built environment is often leveraged for disaster preparedness and response activities. However, factors such as differences in ortho-rectification, atmospheric conditions and human error, results in spatial misalignment between vector data and the timely available RS imagery. Model training for downstream tasks such as object detection, change analysis, etc., is negatively impacted due to such spatial misalignment. Although there has been progress towards automatic alignment of vector data, the lack of scalability remains an open research challenge. This paper proposes to leverage parallel computing to optimize an automatic vector data alignment workflow. It further employs CPU-level multi-core parallelism for improving the performance of the workflow for scalable built environment mapping. We report observations and discuss findings from the preliminary experiments performed on the Summit Supercomputer.

Potnis, Abhishek↗
DOE OSTI2021

A Hybrid System for Learning Classical Data in Quantum States

Deep neural network-powered artificial intelligence has rapidly changed our daily life with various applications. However, as one of the essential steps of deep neural networks, training a heavily-weighted network requires a tremendous amount of computing resources. Especially in the post Moore’s Law era, the limit of semiconductor fabrication technology has restricted the development of learning algorithms to cope with the increasing high intensity training data. Meanwhile, quantum computing has exhibited its significant potential in terms of speeding up the traditionally compute-intensive workloads. For example, Google illustrates quantum supremacy by completing a sampling calculation task in 200 seconds, which is otherwise impracticable on the world’s largest supercomputers. To this end, quantum-based learning becomes an area of interest, with the promising of a quantum speedup. In this paper, we propose GenQu, a hybrid and general-purpose quantum framework for learning classical data through quantum states. We evaluate GenQu with real datasets and conduct experiments on both simulations and real quantum computer IBM-Q. Our evaluation demonstrates that, comparing with classical solutions, the proposed models running on GenQu framework achieve similar accuracy with a much smaller number of qubits, while significantly reducing the parameter size by up to 95.86% and converging speedup by 66.67% faster.

Stein, Samuel A.↗
DOE OSTI2020

Optimizing High Performance Markov Clustering for Pre-Exascale Architectures

HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations and heavily makes use of the sparse matrix-sparse matrix multiplication kernel (SpGEMM). The existing parallel algorithms in HipMCL are not scalable to Exascale architectures, both due to their communication costs dominating the runtime at large concurrencies and also due to their inability to take advantage of accelerators that are increasingly popular. In this work, we systematically remove scalability and performance bottlenecks of HipMCL. We enable GPUs by performing the expensive expansion phase of the MCL algorithm on GPU. Additionally, we propose a CPU-GPU joint distributed SpGEMM algorithm called pipelined Sparse SUMMA and integrate a probabilistic memory requirement estimator that is fast and accurate. Furthermore, we develop a new merging algorithm for the incremental processing of partial results produced by the GPUs, which improves the overlap efficiency and the peak memory usage. We also integrate a recent and faster algorithm for performing SpGEMM on CPUs. We validate our new algorithms and optimizations with extensive evaluations. With the enabling of the GPUs and integration of new algorithms, HipMCL is up to 12.4x faster, being able to cluster a network with 70 million proteins and 68 billion connections just under 15 minutes using 1024 nodes of ORNL's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Efficient I/O for Neural Network Training with Compressed Data

FanStore is a shared object store that enables efficient and scalable neural network training on supercomputers. By providing a global cache layer on node-local burst buffers using a compressed representation, it significantly enhances the processing capability of deep learning (DL) applications on existing hardware. In addition, FanStore allows POSIX-compliant file access to the compressed data in user space. We investigate the tradeoff between runtime overhead and data compression ratio using real-world datasets and applications, and propose a compressor selection algorithm to maximize storage capacity given performance constraints. We consider both asynchronous (i.e., with prefetching) and synchronous I/O strategies, and propose mechanisms for selecting compressors for both approaches. Using FanStore, the same storage hardware can host 2-13x more data for example applications without significant runtime overhead. Empirically, our experiments show that FanStore scales to 512 compute nodes with near linear performance scalability.

Zhang, Zhao↗
DOE OSTI2021

Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale

Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in various graph, scientific computing and machine learning algorithms. In this paper, we consider SpGEMMs performed on hundreds of thousands of processors generating trillions of nonzeros in the output matrix. Distributed SpGEMM at this extreme scale faces two key challenges: (1) high communication cost and (2) inadequate memory to generate the output. Furthermore, we address these challenges with an integrated communication-avoiding and memory-constrained SpGEMM algorithm that scales to 262,144 cores (more than 1 million hardware threads) and can multiply sparse matrices of any size as long as inputs and a fraction of output fit in the aggregated memory. As we go from 16,384 cores to 262,144 cores on a Cray XC40 supercomputer, the new SpGEMM algorithm runs 10x faster when multiplying large-scale protein-similarity matrices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Performance Evaluation of Adaptive Routing on Dragonfly-based Production Systems

Performance of applications in production environments can he sensitive to network congestion. Cray Aries supports adaptively routing each network packet independently based on the load or congestion encountered as a packet traverses the network. Software can dictate different routing policies, adjusting between minimal and non-minimal bias, for each posted message. We have extensively evaluated the sensitivity of the routing bias selection on application performance as well as whole system performance in both production and controlled conditions. We show that the default routing bias used in Aries-based systems is often sub-optimal and that using a higher bias towards minimal routes will not only reduce the congestion effects on the application but also will decrease the overall congestion on the network. This routing scheme results in not only improved mean performance (by up to 12%) of most production applications hut also reduced run-to-run variability. Our study prompted the two supercomputing facilities (ALCF and NERSC) to change the default routing mode on their Aries-based systems. We present the substantial improvement measured in the overall congestion management and interconnect performance in production after making this change.

Chunduri, Sudheer↗
DOE OSTI2021

Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts

Large-scale simulations on nonuniform particle distributions that evolve over time are widely used in cosmology, molecular dynamics, and engineering. Such data are often saved in an unstructured format that neither preserves spatial locality nor provides metadata for accelerating spatial or attribute subset queries, leading to poor performance of visualization tasks. Furthermore, the parallel I/O strategy used typically writes a file per process or a single shared file, neither of which is portable or scalable across different HPC systems. We present a portable technique for scalable, spatially aware adaptive aggregation that preserves spatial locality in the output. We evaluate our approach on two supercomputers, Stampede2 and Summit, and demonstrate that it outperforms prior approaches at scale, achieving up to 2.5× faster writes and reads for nonuniform distributions. Furthermore, the layout written by our method is directly suitable for visual analytics, supporting low-latency reads and attribute-based filtering with little overhead.

Usher, Will↗
DOE OSTI2021

Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs

Cancer is a leading cause of death in the US, second only to heart disease. It is primarily a result of a combination of an estimated two-nine genetic mutations (multi-hit combinations). Although a body of research has identified hundreds of cancer-causing genetic mutations, we don’t know the specific combination of mutations responsible for specific instances of cancer for most cancer types. An approximate algorithm for solving the weighted set cover problem was previously adapted to identify combinations of genes with mutations that may be responsible for individual instances of cancer. However, the algorithm’s computational requirement scales exponentially with the number of genes, making it impractical for identifying more than three-hit combinations, even after the algorithm was parallelized and scaled up to a V100 GPU. Since most cancers have been estimated to require more than three hits, we scaled out the algorithm to identify combinations of four or more hits using 1000 nodes (6000 V100 GPUs with ≈48×106 processing cores) on the Summit supercomputer at Oak Ridge National Laboratory. Efficiently scaling out the algorithm required a series of algorithmic innovations and optimizations for balancing an exponentially divergent workload across processors and for minimizing memory latency and inter-node communication. We achieved an average strong scaling efficiency of 90.14% (80.96%–97.96% for 200 to 1000 nodes), compared to a 100 node run, with 84.18% scaling efficiency for 1000 nodes. With experimental validation, the multi-hit combinations identified here could provide further insight into the etiology of different cancer subtypes and provide a rational basis for targeted combination therapy.

Dash, Sajal↗
DOE OSTI2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data volumes: ideally, methods that can scale data volumes adaptively so as to enable negotiation of performance and fidelity tradeoffs in different situations. Multigrid-based hierarchical data representations hold promise as a solution to this problem, allowing for flexible conversion between different fidelities so that, for example, data can be created at high fidelity and then transferred or stored at lower fidelity via logically simple and mathematically sound operations. However, the effective use of such representations has been hindered until now by the relatively high costs of creating, accessing, reducing, and otherwise operating on such representations. We describe here highly optimized data refactoring kernels for GPU accelerators that enable efficient creation and manipulation of data in multigrid-based hierarchical forms. We demonstrate that our optimized design can achieve up to 250 TB/s aggregated data refactoring throughput—83% of theoretical peak—on 1024 nodes of the Summit supercomputer. We showcase our optimized design by applying it to a large-scale scientific visualization workflow and the MGARD lossy compression software.

Data refactoring↗
DOE OSTI2021

Revisiting Huffman Coding: Toward Extreme Performance on Modern GPU Architectures

Today's high-performance computing (HPC) applications are producing vast volumes of data, which are challenging to store and transfer efficiently during the execution, such that data compression is becoming a critical technique to mitigate the storage burden and data movement cost. Huffman coding is arguably the most efficient Entropy coding algorithm in information theory, such that it could be found as a fundamental step in many modern compression algorithms such as DEFLATE. On the other hand, today's HPC applications are more and more relying on the accelerators such as GPU on supercomputers, while Huffman encoding suffers from low throughput on GPUs, resulting in a significant bottleneck in the entire data processing. In this paper, we propose and implement an efficient Huffman encoding approach based on modern GPU architectures, which addresses two key challenges: (1) how to parallelize the entire Huffman encoding algorithm, including codebook construction, and (2) how to fully utilize the high memory-bandwidth feature of modern GPU architectures. The detailed contribution is fourfold. (1) We develop an efficient parallel codebook construction on GPUs that scales effectively with the number of input symbols. (2) We propose a novel reduction based encoding scheme that can efficiently merge the codewords on GPUs. (3) We optimize the overall GPU performance by leveraging the state-of-the-art CUDA APIs such as Cooperative Groups. (4) We evaluate our Huffman encoder thoroughly using six real-world application datasets on two advanced GPUs and compare with our implemented multi-threaded Huffman encoder. Experiments show that our solution can improve the encoding throughput by up to 5.0x and 6.8x on NVIDIA RTX 5000 and V100, respectively, over the state-of-the-art GPU Huffman encoder, and by up to 3.3x over the multi-thread encoder on two 28-core Xeon Platinum 8280 CPUs.

Tian, Jiannan↗
DOE OSTI2023

DeepThermo: Deep Learning Accelerated Parallel Monte Carlo Sampling for Thermodynamics Evaluation of High Entropy Alloys

Since the introduction of Metropolis Monte Carlo (MC) sampling, it and its variants have become standard tools used for thermodynamics evaluations of physical systems. However, a long-standing problem that hinders the effectiveness and efficiency of MC sampling is the lack of a generic method (a.k.a. MC proposal) to update the system configurations. Consequently, current practices are not scalable. Here we propose a parallel MC sampling framework for thermodynamics evaluation—DeepThermo. By using deep learning–based MC proposals that can globally update the system configurations, we show that DeepThermo can effectively evaluate the phase transition behaviors of high entropy alloys, which have an astronomical configuration space. For the first time, we directly evaluate a density of states expanding over a range of ~e 10,000 for a real material. We also demonstrate DeepThermo’s performance and scalability up to 3,000 GPUs on both NVIDIA V100 and AMD MI250X-based supercomputers.

Yin, Junqi↗
DOE OSTI2024

Drilling Down I/O Bottlenecks with Cross-layer I/O Profile Exploration

I/O performance monitoring tools such as Darshan and Recorder collect I/O-related metrics on production systems and help understand the applications' behavior. However, some gaps prevent end-users from seeing the whole picture when it comes to detecting and drilling down to the root causes of I/O performance slowdowns and where those problems originate. These gaps arise from limitations in the available metrics, their collection strategy, and the lack of translation to actionable items that could advise on optimizations. This paper highlights such gaps and proposes solutions to drill down to the source code level to pinpoint the root causes of I/O bottlenecks scientific applications face by relying on cross-layer analysis combining multiple performance metrics related to I/O software layers. We demonstrate with two real applications how metrics collected in high-level libraries (which are closer to the data models used by an application), enhanced by source-code insights and natural language translations, can help streamline the understanding of I/O behavior and provide guidance to end-users, developers, and supercomputing facilities on how to improve I/O performance. Using this cross-layer analysis and the heuristic recommendations, we attained up to 6.9× speedup from run-as-is executions.

Ather, Hammad↗
DOE OSTI2024

Comparative Study of Large Language Model Architectures on Frontier

Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-trained Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world’s first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.

Yin, Junqi↗
DOE OSTI2025

HPDR: High-Performance Portable Scientific Data Reduction Framework

The rapid growth in scientific data generation is outpacing advancements in computing systems necessary for efficient storage, transfer, and analysis, particularly in the context of exascale computing. With the deployment of first-generation exascale computing systems and next-generation experimental facilities, this gap is widening and necessitates effective data reduction techniques to manage enormous data volumes. Over the past decade, various data reduction methods, including lossless compression, error-controlled lossy compression, and data refactoring, have been developed to accelerate I/O in scientific workflows. Despite significant reductions in data volume, these methods introduce considerable computational overhead, which can become the new bottleneck in data processing. To mitigate this, GPU-accelerated data reduction algorithms have been introduced. However, challenges remain in their integration into exascale workflows, including limited portability across different GPU architectures, substantial memory transfer overhead, and reduced scalability on dense multi-GPU systems. To address these challenges, we propose HPDR, a high-performance and portable data reduction framework. HPDR is designed to enable the execution of state-of-the-art reduction algorithms across diverse processor architectures while reducing memory transfer overhead to 2.3 % of the original, resulting in up to 3.5× faster throughput compared to existing solutions. It also achieves up to 96% of the theoretical speedup in multi-GPU settings. In addition, evaluations on accelerating I/O operations at scale up to 1,024 nodes of the Frontier supercomputer demonstrate that HPDR can achieve up to 103 TB/s reduction throughput, providing up to 4× acceleration in parallel I/O performance compared to existing data reduction routines. This work highlights the potential of HPDR to significantly enhance data reduction efficiency in exascale computing environments.

Chen, Jieyang [University of Oregon]↗