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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 OSTI2012

Approximate Weighted Matching On Emerging Manycore and Multithreaded Architectures

Graph matching is a prototypical combinatorial problem with many applications in computer science and scientific computing, but algorithms for computing optimal matchings are challenging to parallelize. Approximate matching algorithms provide an alternate route for parallelization, and in many contexts compute near-optimal matchings for large-scale graphs. We present sharedmemory parallel implementations for computing half-approximate weighted matching on state-of-the-art multicore (Intel Nehalem and AMD Magny-Cours), manycore (Nvidia Tesla and Nvidia Fermi) and massively multithreaded (Cray XMT) platforms. We provide two implementations: the first implementation uses shared work queues, and is suited to all these platforms; the second implementation is based on dataflow principles, and exploits the architectural features of the Cray XMT. Using a carefully chosen dataset that exhibits characteristics from a wide range of real-world applications, we show scalable performance across different platforms. In particular, for one instance of the input, an R-MAT graph (RMAT-G), we show speedups of: about 32 on 48 cores of an AMD Magny-Cours; 7 on 8 cores of Intel Nehalem; 3 on Nvidia Tesla and 10 on Nvidia Fermi relative to one core of Intel Nehalem; and 60 on 128 processors of Cray XMT. We demonstrate good weak and strong scaling for graphs with up to a billion edges using up to 12, 800 threads. Given the breadth of this work, we focus on simplicity and portability of software rather than excessive fine-tuning for each platform. To the best of our knowledge, this is the first such large-scale study of the half-approximate weighted matching problem on shared-memory platforms. Driven by the critical enabling role of combinatorial algorithms such as matching in scientific computing and the emergence of informatics applications, there is a growing demand to support irregular computations on current and future computing platforms. In this context, we evaluate the capability of emerging multithreaded platforms to tolerate latency induced by irregular memory access patterns, and to support fine-grained parallelism via light-weight synchronization mechanisms. By contrasting the architectural features of these platforms against the Cray XMT, which is specifically designed to support irregular memory-intensive applications, we delineate the impact of these choices on performance.

Halappanavar, Mahantesh↗
DOE OSTI2012

Hands-on Performance Tuning of 3D Finite Difference Earthquake Simulation on GPU Fermi Chipset

3D simulation of earthquake ground motion is one of the most challenging computational problems in science. The emergence of graphic processing units (GPU) as an effective alternative to traditional general purpose processors has become increasingly capable in terms of accelerating scientific computing research. In this paper, we describe our experiences in porting AWP-ODC, a 3D finite difference seismic wave propagation code, to the latest GPU Fermi chipset. We completely rewrote this Fortran-based 13-point asymmetric stencil computation code in C and MPI-CUDA in order to take advantage of the powerful GPU computing capabilities. Our new CUDA code implemented the asymmetric 3D stencil on Fermi to make the best use of GPU on-chip memory for an aggressive parallel efficiency. Benchmark on NVIDIA Tesla M2090 demonstrated 10x speedup versus the original fully optimized AWP-ODC FORTRAN MPI code running on a single Intel Nehalem 2.4 GHz CPU socket (4 cores/CPU), and 15x speedup versus the same MPI code running on a single AMD Istanbul 2.6 GHz CPU socket (6 cores/CPU). Sustained single-GPU performance of 143.8 GFLOPS in single precision is benchmarked for the testing case of 128x128x960 mesh size.

3D Stencil Computation↗
DOE OSTI2012

Multithreaded Algorithms for Maximum Matching in Bipartite Graphs

Abstract—We design, implement, and evaluate algorithms for computing a matching of maximum cardinality in a bipartite graph on multi-core and massively multithreaded computers. As computers with larger number of slower cores dominate the commodity processor market, the design of multithreaded algorithms to solve large matching problems becomes a necessity. Recent work on serial algorithms based on searching for augmenting paths for this problem have shown that their performance is sensitive to the order in which the vertices are processed for matching. In a multithreaded environment, imposing a serial order in which vertices are considered for matching would lead to loss of concurrency and performance. But this raises the question: Would parallel matching algorithms on multithreaded machines improve performance over a serial algorithm? We answer this question in the affirmative. We report efficient multithreaded implementations of two key algorithms (Hopcroft- Karp based on breadth-first-search, and Pothen-Fan based on depth-first-search) and their variants, combined with the Karp- Sipser initialization algorithm. We report extensive results and insights using three shared-memory platforms (a 48-core AMD Opteron, a 32-core Intel Nehalem, and a 128-processor Cray XMT) on a representative set of real-world and synthetic graphs. To the best of our knowledge, this is the first extensive study of augmentation-based parallel algorithms for bipartite cardinality matching.

Azad, Md Ariful↗
DOE OSTI2023

WHONDRS River Corridor Sediment and Water Geochemistry and In Situ Sensor Data from Machine-Learning-Informed Sites across the Contiguous United States (v6)

This dataset supports a broader study examining hyporheic zone respiration rates to improve predictive models at a contiguous United States (CONUS) scale. The CONUS-Scale Model-Sample Study (CM) was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. New machine learning models were created every month to guide sampling locations. Data from the resulting samples were used to test and rebuild the machine learning models for the next round of sampling guidance. Sampling began in April 2022 and ended in October 2023. In addition to the widely distributed CONUS sites, a more spatially focused sampling occurred in the Yakima River Basin, WA in summer 2022. Data from this more spatially intensive sampling occurred under the label “Second Spatial Study (SSS)” and were also included in the machine learning models. Other data types collected from SSS that were not part of CM were published in a separate data package (https://data.ess-dive.lbl.gov/view/doi:10.15485/1969566). This data package was originally published in February 2023. It was updated in June 2023 (v2; new and modified files); December 2023 (v3; new and modified files); June 2024 (v4; new and modified files); April 2024 (v5; new and modified files); and September 2025 (v6; modified files). See the change history section in the readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of two folders of field photos and videos, one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) international generic sample number (IGSN) mapping file; (6) field protocols; (7) a subfolder with sample data; and (8) a subfolder with sensor data. The sample data subfolder contains (1) surface water and sediment dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) surface water and sediment total nitrogen data and averages; (3) surface water major cations and anions and averages; (4) sediment grain size data; (5) sediment iron (II) data and averages; (6) wet sediment mass, dry sediment mass, water mass, and wet sediment volume in incubation and sediment ICR vials; (7) sediment incubation respiration rate data and averages; (8) normalized respiration rate data and averages; (9) methods codes; (10) sediment specific surface area; (11) sediment percent carbon and nitrogen; (12) sediment gravimetric moisture and averages; (15) sediment X-ray diffraction (XRD) data; (16) sediment adenosine triphosphate (ATP) and averages; (17) a subfolder with sediment incubation respiration data, scripts, and plots; (18) surface water and sediment FTICR methods; and (19) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains five subfolders, one containing the sediment .xml data files, one containing the water .xml files, one containing the sediment CoreMS output files, one containing the water CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS).The sensor data subfolder contains (1) a subfolder with miniDOT dissolved oxygen and temperature data and plots; (2) miniDOT dissolved oxygen and temperature summary data; and (3) miniDOT installation methods. All files are .csv, .pdf, .R, .xml, .d, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, .png, .mov, or .mp4. CORRECTION: Carbon and nitrogen content are reported as percentages. The current column headers "01395_C_percent_per_mg" and "01397_N_percent_per_mg" are incorrect. These should read "01395_C_percent" and "01397_N_percent" and will be corrected in the next version of this data package. We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Washington State Parks and Recreation Commission (Scientific Research Permit #210901), and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the samples labeled “SSS” were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview. WHONDRS consortium members were asked to provide any acknowledgments for the collection of samples labeled “CM” and the following is a list of acknowledgments that were submitted with their corresponding Site IDs: (MART) Research activities were conducted in part on the Wind River Experimental Forest within the Gifford Pinchot National Forest; (MP- 100379) Philadelphia is part of Lenapehoking, the ancestral homelands of the Lenape peoples; (MP-102398) Land surveyed is the ancestral homelands of the Nookhose'iinenno (Arapaho), Tsis tsis'tas (Cheyenne), and Nuuchu (Ute); (MP-100749 and MP- 100747) Georgia Coastal Ecosystem LTER, OCE-1832178; (SP-70 and SP-72) Eastern Shoshone, Shoshone-Bannock; (MP- 102944) Funded by Oregon Watershed Enhancement Board. On the traditional lands of the Confederated Tribes of the Siletz, Confederated Tribes of the Grand Rhonde, and the Clatsop-Nehalem Confederated Tribe; (MP- 100607) Holiday Creek is located on the traditional territory of the Monacan Indian Nation; (SP-45) Lafayette Blue Springs State Park; (MP-102420) NSF DEB-2016749; (MP-100019) New Hampshire Agriculture Experiment Station; (SP-35) Rayonier (land owner; https://www.rayonier.com/); (MP- 101276) US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemical Research, Watershed Dynamics and Evolution SFA at ORNL; (MP- 103224) Watershed Dynamics and Evolution SFA at ORNL; (MP- 101584) Traditional lands of the Oceti Sakowin (Dakota, Lakota, Nakoda) and Anishinaabe Peoples.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine learning model inputs, outputs, and scripts associated with “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions” (Malhotra et al., in prep). This effort was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the contiguous United States (CONUS). New machine learning models were created every month to guide sampling locations. Data from the resulting samples were used to test and rebuild the machine learning models for the next round of sampling guidance. Associated sediment and water geochemistry and in situ sensor data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1923689, https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719, and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775. This data package is associated with two GitHub repositories found at https://github.com/parallelworks/dynamic-learning-rivers and https://github.com/WHONDRS-Hub/ICON-ModEx_Open_Manuscript. In addition to this readme, this data package also includes two file-level metadata (FLMD) files that describes each file and two data dictionaries (DD) that describe all column/row headers and variable definitions. This data package consists of two main folders (1) dynamic-learning-rivers and (2) ICON-ModEx_Open_Manuscript which contain snapshots of the associated GitHub repositories. The input data, output data, and machine learning models used to guide sampling locations are within dynamic-learning-rivers. The folder is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning (ML) models trained on the data in “input_data”; (3) “examples” contains files for direct experimentation with the machine learning model, including scripts for setting up “hindcast” run; (4) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; and (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please see the top-level README.md in the GitHub repository for more details on the automation. The scripts and data used to create figures in the manuscript are within ICON-ModEx_Open_Manuscript. The folder is organized into four folders which contain the scripts, data, and pdf for each figure. Within the “fig-model-score-evolution” folder, there is a folder called “intermediate_branch_data” which contains some intermediate files pulled from dynamic-learning-rivers and reorganized to easily integrate into the workflows. NOTE: THIS FOLDER INCLUDES THE FILES AT THE POINT OF PAPER SUBMISSION. IT WILL BE UPDATED ONCE THE PAPER IS ACCEPTED WITH ANY REVISIONS AND WILL INCLUDE A DD/FLMD AT THAT POINT. We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Washington State Parks and Recreation Commission (Scientific Research Permit #210901), and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the samples labeled “SSS” were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview. WHONDRS consortium members were asked to provide any acknowledgments for the collection of samples labeled “CM” and the following is a list of acknowledgments that were submitted with their corresponding Site IDs: (MART) Research activities were conducted in part on the Wind River Experimental Forest within the Gifford Pinchot National Forest; (MP- 100379) Philadelphia is part of Lenapehoking, the ancestral homelands of the Lenape peoples; (MP-102398) Land surveyed is the ancestral homelands of the Nookhose'iinenno (Arapaho), Tsis tsis'tas (Cheyenne), and Nuuchu (Ute); (MP-100749 and MP- 100747) Georgia Coastal Ecosystem LTER, OCE-1832178; (SP-70 and SP-72) Eastern Shoshone, Shoshone-Bannock; (MP- 102944) Funded by Oregon Watershed Enhancement Board. On the traditional lands of the Confederated Tribes of the Siletz, Confederated Tribes of the Grand Rhonde, and the Clatsop-Nehalem Confederated Tribe; (MP- 100607) Holiday Creek is located on the traditional territory of the Monacan Indian Nation; (SP-45) Lafayette Blue Springs State Park; (MP-102420) NSF DEB-2016749; (MP-100019) New Hampshire Agriculture Experiment Station; (SP-35) Rayonier (land owner; https://www.rayonier.com/); (MP- 101276) US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemical Research, Watershed Dynamics and Evolution SFA at ORNL; (MP- 103224) Watershed Dynamics and Evolution SFA at ORNL; (MP- 101584) Traditional lands of the Oceti Sakowin (Dakota, Lakota, Nakoda) and Anishinaabe Peoples.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Implementation and Optimization of miniGMG - a Compact Geometric Multigrid Benchmark

Multigrid methods are widely used to accelerate the convergence of iterative solvers for linear systems used in a number of different application areas. In this report, we describe miniGMG, our compact geometric multigrid benchmark designed to proxy the multigrid solves found in AMR applications. We explore optimization techniques for geometric multigrid on existing and emerging multicore systems including the Opteron-based Cray XE6, Intel Sandy Bridge and Nehalem-based Infiniband clusters, as well as manycore-based architectures including NVIDIA's Fermi and Kepler GPUs and Intel's Knights Corner (KNC) co-processor. This report examines a variety of novel techniques including communication-aggregation, threaded wavefront-based DRAM communication-avoiding, dynamic threading decisions, SIMDization, and fusion of operators. We quantify performance through each phase of the V-cycle for both single-node and distributed-memory experiments and provide detailed analysis for each class of optimization. Results show our optimizations yield significant speedups across a variety of subdomain sizes while simultaneously demonstrating the potential of multi- and manycore processors to dramatically accelerate single-node performance. However, our analysis also indicates that improvements in networks and communication will be essential to reap the potential of manycore processors in large-scale multigrid calculations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Aho-Corasick String Matching on Shared and Distributed Memory Parallel Architectures

String matching is at the core of many critical applications, including network intrusion detection systems, search engines, virus scanners, spam filters, DNA and protein sequencing, and data mining. For all of these applications string matching requires a combination of (sometimes all) the following characteristics: high and/or predictable performance, support for large data sets and flexibility of integration and customization. Many software based implementations targeting conventional cache-based microprocessors fail to achieve high and predictable performance requirements, while Field-Programmable Gate Array (FPGA) implementations and dedicated hardware solutions fail to support large data sets (dictionary sizes) and are difficult to integrate and customize. The advent of multicore, multithreaded, and GPU-based systems is opening the possibility for software based solutions to reach very high performance at a sustained rate. This paper compares several software-based implementations of the Aho-Corasick string searching algorithm for high performance systems. We discuss the implementation of the algorithm on several types of shared-memory high-performance architectures (Niagara 2, large x86 SMPs and Cray XMT), distributed memory with homogeneous processing elements (InfiniBand cluster of x86 multicores) and heterogeneous processing elements (InfiniBand cluster of x86 multicores with NVIDIA Tesla C10 GPUs). We describe in detail how each solution achieves the objectives of supporting large dictionaries, sustaining high performance, and enabling customization and flexibility using various data sets.

99 GENERAL AND MISCELLANEOUS↗