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NASA NTRS2010

Symbolic Analysis of Concurrent Programs with Polymorphism

The current trend of multi-core and multi-processor computing is causing a paradigm shift from inherently sequential to highly concurrent and parallel applications. Certain thread interleavings, data input values, or combinations of both often cause errors in the system. Systematic verification techniques such as explicit state model checking and symbolic execution are extensively used to detect errors in such systems [7, 9]. Explicit state model checking enumerates possible thread schedules and input data values of a program in order to check for errors [3, 9]. To partially mitigate the state space explosion from data input values, symbolic execution techniques substitute data input values with symbolic values [5, 7, 6]. Explicit state model checking and symbolic execution techniques used in conjunction with exhaustive search techniques such as depth-first search are unable to detect errors in medium to large-sized concurrent programs because the number of behaviors caused by data and thread non-determinism is extremely large. We present an overview of abstraction-guided symbolic execution for concurrent programs that detects errors manifested by a combination of thread schedules and data values [8]. The technique generates a set of key program locations relevant in testing the reachability of the target locations. The symbolic execution is then guided along these locations in an attempt to generate a feasible execution path to the error state. This allows the execution to focus in parts of the behavior space more likely to contain an error.

Rungta, Neha Shyam↗

NASA NTRS2012

Exploratory Climate Data Visualization and Analysis Using DV3D and UVCDAT

Earth system scientists are being inundated by an explosion of data generated by ever-increasing resolution in both global models and remote sensors. Advanced tools for accessing, analyzing, and visualizing very large and complex climate data are required to maintain rapid progress in Earth system research. To meet this need, NASA, in collaboration with the Ultra-scale Visualization Climate Data Analysis Tools (UVCOAT) consortium, is developing exploratory climate data analysis and visualization tools which provide data analysis capabilities for the Earth System Grid (ESG). This paper describes DV3D, a UV-COAT package that enables exploratory analysis of climate simulation and observation datasets. OV3D provides user-friendly interfaces for visualization and analysis of climate data at a level appropriate for scientists. It features workflow inte rfaces, interactive 40 data exploration, hyperwall and stereo visualization, automated provenance generation, and parallel task execution. DV30's integration with CDAT's climate data management system (COMS) and other climate data analysis tools provides a wide range of high performance climate data analysis operations. DV3D expands the scientists' toolbox by incorporating a suite of rich new exploratory visualization and analysis methods for addressing the complexity of climate datasets.

Maxwell, Thomas↗

NASA NTRS2013

Comparison of Precision of Biomass Estimates in Regional Field Sample Surveys and Airborne LiDAR-Assisted Surveys in Hedmark County, Norway

Airborne scanning LiDAR (Light Detection and Ranging) has emerged as a promising tool to provide auxiliary data for sample surveys aiming at estimation of above-ground tree biomass (AGB), with potential applications in REDD forest monitoring. For larger geographical regions such as counties, states or nations, it is not feasible to collect airborne LiDAR data continuously ("wall-to-wall") over the entire area of interest. Two-stage cluster survey designs have therefore been demonstrated by which LiDAR data are collected along selected individual flight-lines treated as clusters and with ground plots sampled along these LiDAR swaths. Recently, analytical AGB estimators and associated variance estimators that quantify the sampling variability have been proposed. Empirical studies employing these estimators have shown a seemingly equal or even larger uncertainty of the AGB estimates obtained with extensive use of LiDAR data to support the estimation as compared to pure field-based estimates employing estimators appropriate under simple random sampling (SRS). However, comparison of uncertainty estimates under SRS and sophisticated two-stage designs is complicated by large differences in the designs and assumptions. In this study, probability-based principles to estimation and inference were followed. We assumed designs of a field sample and a LiDAR-assisted survey of Hedmark County (HC) (27,390 km2), Norway, considered to be more comparable than those assumed in previous studies. The field sample consisted of 659 systematically distributed National Forest Inventory (NFI) plots and the airborne scanning LiDAR data were collected along 53 parallel flight-lines flown over the NFI plots. We compared AGB estimates based on the field survey only assuming SRS against corresponding estimates assuming two-phase (double) sampling with LiDAR and employing model-assisted estimators. We also compared AGB estimates based on the field survey only assuming two-stage sampling (the NFI plots being grouped in clusters) against corresponding estimates assuming two-stage sampling with the LiDAR and employing model-assisted estimators. For each of the two comparisons, the standard errors of the AGB estimates were consistently lower for the LiDAR-assisted designs. The overall reduction of the standard errors in the LiDAR-assisted estimation was around 40-60% compared to the pure field survey. We conclude that the previously proposed two-stage model-assisted estimators are inappropriate for surveys with unequal lengths of the LiDAR flight-lines and new estimators are needed. Some options for design of LiDAR-assisted sample surveys under REDD are also discussed, which capitalize on the flexibility offered when the field survey is designed as an integrated part of the overall survey design as opposed to previous LiDAR-assisted sample surveys in the boreal and temperate zones which have been restricted by the current design of an existing NFI.

Comparison↗

NASA NTRSDate not supplied

Multi-Spectral Lidar Observations and Balloon Borne Validation of SO 2 -O 3 During the SOWLETS Campaign: An Examination of Local Incinerator Plume

The Langley Mobile O3 Lidar (LMOL) was stationed at NASA's Langley Research Center for the initiation of the SO 2 -O 3 Water Land Environment study (SOWLETS). The primary focus of the campaign was to examine the capabilities of a novel four-wavelength detection technique to measure the concentrations of sulfur dioxide (SO2) and ozone (O3). The exact location of the lidar, near the NASA/CAPABLE site, was optimized to intercept the plume emissions from a proximate incinerator facility using historical weather data for the month of the campaign. A novel four-wavelength lidar technique focused on the detection of sulfur dioxide (SO2) and ozone (O3) was employed, and its capabilities were thoroughly examined. The technique is built upon the standard DIAL. While 3 wavelengths would be enough to retrieve both SO2 and O3, the 4 wavelengths allow to provide data on aerosol backscattering. In parallel, SO 2 -O 3 sondes were launched and installed in the nearby NASA Landing and Impact research facility, providing validation for the lidar's atmospheric measurements. In conclusion, this campaign offers an improved understanding of SO2 emissions in the local environment and a validation of a novel technique to facilitate pollution observations. It shows the promise of this new kind of lidar to better understand and validate the observations by NASA/TEMPO ("Tropospheric Emissions: Monitoring of Pollution").

G. Gronoff↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter]

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particles and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Big Data Mining for Applied Energy Savings in Buildings

Residential and commercial buildings in China, India, the United States (US), United Kingdom (UK), and Italy consume 39-45% of each nation's primary energy (approximately 73% of electricity). Building energy models can be used to automatically optimize the return-on-investment for retrofits to improve a building’s energy efficiency. However, with an average of 3,000 building descriptors necessary to accurately simulate a single building, there is a market need to reduce the transaction cost for creating a simulatable model for every building in a city and calibrate the models to utility data prior to capital expenditures. Oak Ridge National Laboratory has utilized two of the world’s fastest supercomputers, assembled unique datasets, and developed innovative algorithms for big data mining to produce the Automatic detection and creation of Building Energy Models (AutoBEM) technology for urban-scale energy modeling. The project developed the world’s most accurate method for determining building footprints from satellite imagery and the world’s fastest building energy model generator. The team has also leveraged a total of eight supercomputers to analyze the best methods, metrics, and algorithms for calibrating building models to measured data within 4% of hourly electricity use; well beyond current industry standards necessary for private-sector financing. The project developed the world’s fastest buildings simulator, over 8 million simulations totaling over 200TB, and mined this data with over 130,000 parallel artificial intelligence algorithmic instances to develop the world’s best calibration algorithm in terms of accuracy, runtime, and robustness.

New, Joshua↗

DOE OSTI2025

Design and Construction of a High-Resolution Hodoscope for the GlueX Experiment with High-Statistics Analysis of the p0, ¿, and ¿1 Photoproduction Cross Sections from the RadPhi Experiment

Differential cross sections for forward-angle photoproduction of p0, ¿, and ¿ 1 pseudoscalar mesons were measured using data from the RadPhi experiment conducted in Hall B at Jef ferson Lab. RadPhi utilized a tagged bremsstrahlung photon beam incident on a stationary 9Be target, with a detector system configured to trigger on a recoil proton in coincidence with multiple neutral showers in the calorimeter. Events were reconstructed and subjected to kinematic constraints, with background suppressed via sideband subtraction guided by Monte Carlo modeling of background contributions. Cross sections were extracted over the photon energy range 4.4– 5.4 GeV and binned in invariant momentum transfer t, providing measurements from one of the first high-statistics experiments of forward ¿ and ¿1 pro duction from a nuclear target at these energies. Acceptance corrections were applied using a detailed GEANT-based simulation of the detector geometry and response. The resulting cross sections are consistent with 2020 CLAS results, when scaled by the number of protons in beryllium, and show broad agreement with other data and theoretical models. In parallel, a high-resolution photon tagger detector, the Tagger Microscope (TAGM), was designed, constructed, and commissioned for the GlueX experiment in Hall D at Jefferson Lab. The TAGM was developed to provide high-rate tagging capability in the coherent bremsstrahlung peak by detecting post-bremsstrahlung electrons across a one GeV range along the focal plane of the tagging spectrometer. The detector consists of a 5ˆ102 array of 2ˆ2 mm2 square BCF-20 plastic scintillating fibers thermally fused to BCF-98 light guide fibers optically coupled to silicon photomultipliers. These fibers are mounted in a precision machined framework enabling fine positional adjustments to maintain precise alignment with post-bremsstrahlung electron trajectories, while ensuring mechanical rigidity, thermal stability, optical isolation, minimal inactive area, and radiation shielding for electronics. The construction effort involved extensive testing of fiber quality, light transmission, thermal fusing, radiation hardness, and defect analysis using SEM and EDX techniques. Following its installation and commissioning, the TAGM became a critical component of the GlueX beamline, enabling high-rate tagging essential for studies of hybrid mesons and gluonic ex citations.

McIntyre, James [Univ. of Connecticut, Storrs, CT ↗

DOE OSTI2017

Parallel variable selection for effective performance prediction

Large data analysis problems often involve a large number of variables, and the corresponding analysis algorithms may examine all variable combinations to find the optimal solution. For example, to model the time required to complete a scientific workflow, we need to consider the impact of dozens of parameters. To reduce the model building time and reduce the likelihood of overfitting, we look to variable selection methods to identify the critical variables for the performance model. In this work, we create a combination of variable selection and performance prediction methods that is as effective as the exhaustive search approach when the exhaustive search could be completed in a reasonable amount of time. To handle the cases where the exhaustive search is too time consuming, we develop the parallelized variable selection algorithm. Additionally, we develop a parallel grouping mechanism that further reduces the variable selection time by 70%.As a case study, we exercise the variable selection technique with the performance measurement data from the Palomar Transient Factory (PTF) workflow. The application scientists have determined that about 50 variables and parameters are important to the performance of the workflows. Our tests show that the Sequential Backward Selection algorithm is able to approximate the optimal subset relatively quickly. By reducing the number of variables used to build the model from 50 to 4, we are able to maintain the prediction quality while reducing the model building time by a factor of 6. Using the parallelization and grouping techniques we developed in this work, the variable selection process was reduced from over 18 hours to 15 minutes while ending up with the same variable subset.

Wang, J↗

NASA NTRS1993

Parallel Consensual Neural Networks

A new neural network architecture is proposed and applied in classification of remote sensing/geographic data from multiple sources. The new architecture is called the parallel consensual neural network and its relation to hierarchical and ensemble neural networks is discussed. The parallel consensual neural network architecture is based on statistical consensus theory. The input data are transformed several times and the different transformed data are applied as if they were independent inputs and are classified using stage neural networks. Finally, the outputs from the stage networks are then weighted and combined to make a decision. Experimental results based on remote sensing data and geographic data are given. The performance of the consensual neural network architecture is compared to that of a two-layer (one hidden layer) conjugate-gradient backpropagation neural network. The results with the proposed neural network architecture compare favorably in terms of classification accuracy to the backpropagation method.

Benediktsson, J. A.↗

DOE OSTI2019

Parallel Computing for Module-Based Computational Experiment

Large-scale scientific code plays an important role in scientific researches. In order to facilitate module and element evaluation in scientific applications, we introduce a unit testing framework and describe the demand for module-based experiment customization. We then develop a parallel version of the unit testing framework to handle long-term simulations with a large amount of data. Specifically, we apply message passing based parallelization and I/O behavior optimization to improve the performance of the unit testing framework and use profiling result to guide the parallel process implementation. Finally, we present a case study on litter decomposition experiment using a standalone module from a large-scale Earth System Model. This case study is also a good demonstration on the scalability, portability, and high-efficiency of the framework.

Yao, Zhuo↗

DOE OSTI2024

Parallel Randomized Tucker Decomposition Algorithms

The Tucker tensor decomposition is a natural extension of the singular value decomposition (SVD) to multiway data. Here, we propose to accelerate Tucker tensor decomposition algorithms by using randomization and parallelization. We present two algorithms that scale to large data and many processors, significantly reduce both computation and communication cost compared to previous deterministic and randomized approaches, and obtain nearly the same approximation errors. The key idea in our algorithms is to perform randomized sketches with Kronecker-structured random matrices, which reduces computation compared to unstructured matrices and can be implemented using a fundamental tensor computational kernel. We provide probabilistic error analysis of our algorithms and implement a new parallel algorithm for the structured randomized sketch. Our experimental results demonstrate that our combination of randomization and parallelization achieves accurate Tucker decompositions much faster than alternative approaches. We observe up to a 16X speedup over the fastest deterministic parallel implementation on 3D simulation data.

Tucker decompositions↗

DOE OSTI2025

Data-Driven Compositional Optimization in Misspecified Regimes

With a manifold growth in the scale and intricacy of systems, the challenges of parametric misspecification become pronounced. These concerns are further exacerbated in compositional settings, which emerge in problems complicated by modeling risk and robustness. In “Data-Driven Compositional Optimization in Misspecified Regimes,” the authors consider the resolution of compositional stochastic optimization problems, plagued by parametric misspecification. In considering settings where such misspecification may be resolved via a parallel learning process, the authors develop schemes that can contend with diverse forms of risk, dynamics, and nonconvexity. They provide asymptotic and rate guarantees for unaccelerated and accelerated schemes for convex, strongly convex, and nonconvex problems in a two-level regime with extensions to the multilevel setting. Surprisingly, the nonasymptotic rate guarantees show no degradation from the rate statements obtained in a correctly specified regime and the schemes achieve optimal (or near-optimal) sample complexities for general T-level strongly convex and nonconvex compositional problems.

Business & Economics↗

DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

A Partitioned - Task Parallel Implementation of the NASA Multiscale Analysis Tool for High Performance Computing

The NASA Multiscale Analysis Tool (NASMAT) is a platform for multiscale modeling of composites which can perform analysis of materials with any arbitrary number of length scales. The platform supports modularity, scalability, and interoperability using recursive procedures and data structures. A Macro solver driven parallelization scheme often limits the capability of NASMAT to scale as it has access to limited memory and number of cores (often one core/thread) and often forces to implement macro solver specific changes to the platform. In this work, a partitioned task-parallel approach is adopted, where the parallelization strategy adopted for NASMAT is independent of the macro solver and the computational resources are managed independently. The programming architecture takes into account the hierarchy of multiple scales (task-dependence) and the heterogeneous nature (dynamic load balancing) of computation through implementation of a hierarchy-informed task parallel model. The partitioned nature of the framework further extends the “plug and play” capability of NASMAT. preCICE, an open-source library for coupling multiphysics solver in a partitioned manner, is adopted to integrate NASMAT with an external macro solver by implementing a NASMAT adapter for preCICE. Speedup and scalability of the framework is studied for micromechanical models of varying size.

task-parallel↗

DOE OSTI2024

Investigation of Benchmark $k$ eff Sensitivity and Uncertainty for 239 Pu fission in Specific Energy Ranges

Nuclear data at intermediate energies (from 1 to 100s of keV) are evaluated based on scarce differential data and theory unable to capture physics’ expected structure. There is also a lack of integral data. This is a known deficiency and is challenging to address. Calculated effective multiplication factor, k eff , values for intermediate energy experiments are ~25× further from experiment than for fast energies and are often well outside the experimental uncertainties. The goal of the PARADIGM (PARallel Approach of Differential and InteGral Measurements) project is to significantly re duce the uncertainties of intermediate energy nuclear data for 239 Pu. To this end, PARADIGM simultaneously optimizes experiments at both the Los Alamos Neutron Science Center (LANSCE) and National Criticality Experiments Research Center (NCERC). The combined set of data will inform new intermediate-energy nuclear data. By execution of differential and integral experiments, establishment of new theory, and undertaking nuclear data evaluation in parallel, the timeline to deliver improved nuclear data to users will be reduced significantly that is to three years. For the PARADIGM project, it was decided to optimize an integral experiment for two neutron energy ranges, within the full intermediate energy range. The low energy range goes from 1 to 30 keV, while the higher energy range goes from 30 to 600 keV. This work focuses on nuclear data sensitivities and uncertainties for 239 Pu fission for existing experiments in the International Criticality Safety Benchmark Evaluation Project (ICSBEP). When designing new experiments, it is important to understand what benchmarks currently exist. For a more traditional experiment design (in which a specific application model(s) exists), comparisons would be made between the application model(s) and existing benchmarks. For PARADIGM, there is no specific application model, but instead the specific nuclear data reaction and energy ranges of interest can be explored for existing benchmarks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

nbodykit: An Open-source, Massively Parallel Toolkit for Large-scale Structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface, we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, two- and three-point correlation functions, a friends-of-friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enables nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high-performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Collectively loading programs in a multiple program multiple data environment

Techniques are disclosed for loading programs efficiently in a parallel computing system. In one embodiment, nodes of the parallel computing system receive a load description file which indicates, for each program of a multiple program multiple data (MPMD) job, nodes which are to load the program. The nodes determine, using collective operations, a total number of programs to load and a number of programs to load in parallel. The nodes further generate a class route for each program to be loaded in parallel, where the class route generated for a particular program includes only those nodes on which the program needs to be loaded. For each class route, a node is selected using a collective operation to be a load leader which accesses a file system to load the program associated with a class route and broadcasts the program via the class route to other nodes which require the program.

97 MATHEMATICS AND COMPUTING↗