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At least 829 records · Page 46

Parallel processing implementations of a contextual classifier for multispectral remote sensing data

Contextual classifiers are being developed as a method to exploit the spatial/spectral context of a pixel to achieve accurate classification. Classification algorithms such as the contextual classifier typically require large amounts of computation time. One way to reduce the execution time of these tasks is through the use of parallelism. The applicability of the CDC flexible processor system and of a proposed multimicroprocessor system (PASM) for implementing contextual classifiers is examined.

Siegel, H. J.↗

A comment on the position dependent diffusion coefficient representation of structural heterogeneity

Experimental studies of the variation of the mean square displacement (MSD) of a particle in a confined colloid suspension that exhibits density variations on the scale length of the particle diameter are not in agreement with the prediction that the spatial variation in MSD should mimic the spatial variation in density. The predicted behavior is derived from the expectation that the MSD of a particle depends on the system density and the assumption that the force acting on a particle is a point function of position. The experimental data are obtained from studies of the MSDs of particles in narrow ribbon channels and between narrowly spaced parallel plates and from new data, reported herein, of the radial and azimuthal MSDs of a colloid particle in a dense colloid suspension confined to a small circular cavity. In each of these geometries, a dense colloid suspension exhibits pronounced density oscillations with spacing of a particle diameter. We remove the discrepancy between prediction and experiment using the Fisher-Methfessel interpretation of how local equilibrium in an inhomogeneous system is maintained to argue that the force acting on a particle is delocalized over a volume with radius equal to a particle diameter. Our interpretation has relevance to the relationship between the scale of inhomogeneity and the utility of translation of the particle MSD into a position dependent diffusion coefficient and to the use of a spatially dependent diffusion coefficient to describe mass transport in a heterogeneous system.

74 ATOMIC AND MOLECULAR PHYSICS↗

FasTensor (FT) v0.0.1

The FasTensor implements the native array data programming mode namely SLOPE for modern data analysis tasks. It is designed to work in parallel on supercomputer and can handle terabyte data analysis tasks. It is thousand times faster than other data analysis systems such as Apache Spark and 38% faster than TensorFlow in dealing with large scale scientific data analysis. It has wide applications in image data analysis and mesh data analysis tasks in physical simulations and other fields.

Wu, Kesheng↗

4BMS-X Design and Test Activation

In support of the NASA goals to reduce power, volume and mass requirements on future CO2 (Carbon Dioxide) removal systems for exploration missions, a 4BMS (Four Bed Molecular Sieve) test bed was fabricated and activated at the NASA Marshall Space Flight Center. The 4BMS-X (Four Bed Molecular Sieve-Exploration) test bed used components similar in size, spacing, and function to those on the flight ISS flight CDRA system, but were assembled in an open framework. This open framework allows for quick integration of changes to components, beds and material systems. The test stand is highly instrumented to provide data necessary to anchor predictive modeling efforts occurring in parallel to testing. System architecture and test data collected on the initial configurations will be presented.

Peters, Warren T.↗

Dynamic Load Balancing For Grid Partitioning on a SP-2 Multiprocessor: A Framework

Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a framework is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single IBM SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine IBM SP2.

Sohn, Andrew↗

Dynamic Load Balancing for Grid Partitioning on a SP-2 Multiprocessor: A Framework

Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a framework is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single EBM SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine IBM SP2.

Sohn, Andrew↗

Dynamic Load Balancing for Finite Element Calculations on Parallel Computers

Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a frame work is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine SP2.

Pramono, Eddy↗

Feed-forward volume rendering algorithm for moderately parallel MIMD machines

Algorithms for direct volume rendering on parallel and vector processors are investigated. Volumes are transformed efficiently on parallel processors by dividing the data into slices and beams of voxels. Equal sized sets of slices along one axis are distributed to processors. Parallelism is achieved at two levels. Because each slice can be transformed independently of others, processors transform their assigned slices with no communication, thus providing maximum possible parallelism at the first level. Within each slice, consecutive beams are incrementally transformed using coherency in the transformation computation. Also, coherency across slices can be exploited to further enhance performance. This coherency yields the second level of parallelism through the use of the vector processing or pipelining. Other ongoing efforts include investigations into image reconstruction techniques, load balancing strategies, and improving performance.

Yagel, Roni↗

Plasma and energetic particle structure upstream of a quasi-parallel interplanetary shock

ISEE 1, 2 and 3 data from 1978 on interplanetary magnetic fields, shock waves and particle energetics are examined to characterize a quasi-parallel shock. The intense shock studied exhibited a 640 km/sec velocity. The data covered 1-147 keV protons and electrons and ions with energies exceeding 30 keV in regions both upstream and downstream of the shock, and also the magnitudes of ion-acoustic and MHD waves. The energetic particles and MHD waves began being detected 5 hr before the shock. Intense halo electron fluxes appeared ahead of the shock. A closed magnetic field structure was produced with a front end 700 earth radii from the shock. The energetic protons were cut off from the interior of the magnetic bubble, which contained a markedly increased density of 2-6 keV protons as well as the shock itself.

Kennel, C. F.↗

Data flow modeling techniques

There have been a number of simulation packages developed for the purpose of designing, testing and validating computer systems, digital systems and software systems. Complex analytical tools based on Markov and semi-Markov processes have been designed to estimate the reliability and performance of simulated systems. Petri nets have received wide acceptance for modeling complex and highly parallel computers. In this research data flow models for computer systems are investigated. Data flow models can be used to simulate both software and hardware in a uniform manner. Data flow simulation techniques provide the computer systems designer with a CAD environment which enables highly parallel complex systems to be defined, evaluated at all levels and finally implemented in either hardware or software. Inherent in data flow concept is the hierarchical handling of complex systems. In this paper we will describe how data flow can be used to model computer system.

Kavi, K. M.↗

MLtool++ package for machine learning and its applications to materials data

We are developing Mltool++ package of software programs for machine learning (ML). Given the MLtool Python code, we create a faster C++ code with the potential for parallelization. We have extracted materials data from the literature. One dataset contains melting temperatures of stoichiometric 1:1 metallic compounds XZ, composed by elements X={Al, Ti, V, Cr, Zr, Nb, Mo, Hf, Ta, W} and Z={Co, Ni, Cu, Rh, Pd, Ag, Ir, Pt, Au}, and another contains solid-solid symmetry-breaking phase transition temperatures. We studied dependences of temperatures on composition, found several correlations, and parametrized them by analytical functions. Mltool++ package is generic and applicable to any tabulated numeric data.

Pierce M. Pettit↗

Developing Ultrahigh-Resolution E3SM Land Model for GPU Systems

Designing and refactoring complex scientific code, such as the E3SM land model (ELM), for new computing architectures is challenging. This paper presents design strategies and technical approaches to develop a data-oriented, GPU-ready ELM model using compiler directives (OpenACC/OpenMP). We first analyze the datatypes and processes in the original ELM code. Then we present design considerations for ultrahigh-resolution ELM (uELM) development for massive GPU systems. These techniques include the global data-oriented simulation workflow, domain partition, code porting and data copy, memory reduction, parallel loop restructure and flattening, and race condition detection. We implemented the first version of uELM using OpenACC targeting the NVidia GPUs in the Summit supercomputer at Oak Ridge National Laboratory. During the implementation, we developed a software tool (named SPEL) to facilitate code generation, verification, and performance tuning using these techniques. The first uELM implementation for Nvidia GPUs on Summit delivered promising results: 1) over 98% of the ELM code was automatically generated and tuned by scripts. Most ELM modules had better computational performances than the original ELM code for CPUs. The GPU-ready uELM is more scalable than the CPU code on fully-loaded Summit nodes. Example profiling results from several modules are also presented to illustrate the performance improvements and race condition detection. The lessons learned and toolkit developed in the study are also suitable for further uELM deployment using OpenMP on the first US exascale computer, Frontier, equipped with AMD CPUs and GPUs.

Schwartz, Peter↗

A Parametric, Data-Driven, Non-Intrusive Reduced-Order Model Framework for Crystal Plasticity Simulations of Voids

The influence of the internal structure at micrometer length scales on the deformation of polycrystalline materials can be effectively captured using crystal plasticity finite element methods (CPFEM). However, the complexity and nonlinearity of the deformation equations CPFEM solves demand significant computational power and resources to achieve accurate predictions, limiting its broader application. To address this challenge, we have identified a reduced-order representation of the complex data in order to establish a computationally efficient reduced-order models (ROM) and drastically reduce the computational expense of CPFEM. Specifically, in this work, we developed a parametric, data-driven, and non-intrusive ROM framework for CPFEM using proper orthogonal decomposition (POD) and sparse variational Gaussian process (SVGP) regression for single-crystal microstructures under tensile loading conditions. The developed protocol enables one to compress field into a latent/low-dimensional space described by principal component analysis (PCA) via the singular value decomposition (SVD) algorithm. As a result, the high-dimensional data are reduced to a significantly smaller amount of dimensions with POD bases and POD coefficients. Furthermore, we deployed an ensemble of SVGPs—extended from the classical Gaussian process (GP) regression for scalability and handling big data—in a massively parallel manner to train and predict latent POD coefficients using known POD bases from a set of previously obtained simulations results. Lastly, using the predicted POD coefficients, we reconstructed the full-field results and showed reasonable agreement compared with the true values obtained from running CPFEM. The developed framework is validated with a set of CPFEM simulations of a single embedded void in single-crystal aluminum alloy. While the framework is broadly applicable, this work specifically focuses on single-crystal microstructures, a single load case (e.g., tensile), and a specific void geometry (spherical).

Anisotropy↗

Exploring performance and energy tradeoffs for irregular applications: A case study on the Tilera many-core architecture

High performance, parallel applications with irregular data accesses are becoming a critical workload class for modern systems. In particular, the execution of such workloads on emerging many-core systems is expected to be a significant component of applications in data mining, machine learning, scientific computing and graph analytics. However, power and energy constraints limit the capabilities of individual cores, memory hierarchy and on-chip interconnect of such systems, thus leading to architectural and software trade-os that must be understood in the context of the intended application’s behavior. Irregular applications are notoriously hard to optimize given their data-dependent access patterns, lack of structured locality and complex data structures and code patterns. We have ported two irregular applications, graph community detection using the Louvain method (Grappolo) and high-performance conjugate gradient (HPCCG), to the Tilera many-core system and have conducted a detailed study of platform-independent and platform-specific optimizations that improve their performance as well as reduce their overall energy consumption. To conduct this study, we employ an auto-tuning based approach that explores the optimization design space along three dimensions - memory layout schemes, GCC compiler flag choices and OpenMP loop scheduling options. We leverage MIT’s OpenTuner auto-tuning framework to explore and recommend energy optimal choices for different combinations of parameters. We then conduct an in-depth architectural characterization to understand the memory behavior of the selected workloads. Finally, we perform a correlation study to demonstrate the interplay between the hardware behavior and application characteristics. Using auto-tuning, we demonstrate whole-node energy savings and performance improvements of up to 49:6% and 60% relative to a baseline instantiation, and up to 31% and 45:4% relative to manually optimized variants.

auto tuning↗

Reduction of hexavalent chromium by fasted and fed human gastric fluid. I. Chemical reduction and mitigation of mutagenicity

Evaluation of the reducing capacity of human gastric fluid from healthy individuals, under fasted and fed conditions, is critical for assessing the cancer hazard posed by ingested hexavalent chromium [Cr(VI)] and for developing quantitative physiologically-based pharmacokinetic models used in risk assessment. In the present study, the patterns of Cr(VI) reduction were evaluated in 16 paired pre- and post-meal gastric fluid samples collected from 8 healthy volunteers. Human gastric fluid was effective both in reducing Cr(VI), as measured by using the s-diphenylcarbazide colorimetric method, and in attenuating mutagenicity in the Ames test. The mean (± SE) Cr(VI)-reducing ability of post-meal samples (20.4 ± 2.6 μg Cr(VI)/mL gastric fluid) was significantly higher than that of pre-meal samples (10.2 ± 2.3 μg Cr(VI)/mL gastric fluid). When using the mutagenicity assay, the decrease of mutagenicity produced by pre-meal and post-meal samples corresponded to reduction of 13.3 ± 1.9 and 25.6 ± 2.8 μg Cr(VI)/mL gastric fluid, respectively. These data are comparable to parallel results conducted by using speciated isotope dilution mass spectrometry. Cr(VI) reduction was rapid, with > 70% of total reduction occurring within 1 min and 98% of reduction is achieved within 30 min with post-meal gastric fluid at pH 2.0. pH dependence was observed with decreasing Cr(VI) reducing capacity at higher pH. Attenuation of the mutagenic response is consistent with the lack of DNA damage observed in the gastrointestinal tract of rodents following administration of ≤ 180 ppm Cr(VI) for up to 90 days in drinking water. Quantifying Cr(VI) reduction kinetics in the human gastrointestinal tract is necessary for assessing the potential hazards posed by Cr(VI) in drinking water. - Highlights: • Cr(VI) reduction capacity was greater in post-meal than paired pre-meal samples. • Cr(VI) reduction was rapid, pH dependent, and due to heat stable components. • Gastric fluid attenuates the mutagenicity of Cr(VI) and reduces risk of GI cancer. • The results are useful to quantitatively evaluate the fate of ingested Cr(VI).

60 APPLIED LIFE SCIENCES↗

Pillars of Cloud-Based Earth Observation Science Education

Earth observation (EO) is undergoing a paradigm shift with the development of cloud-based analytical platforms supporting EO data collection and access, parallel processing, easier communication of results, and expanded accessibility. As the global community of users and the diversity of applications grow, there is a clear need for expanded educational capacity to leverage these developments and increase the impact of EO research and teaching. Drawing upon extensive conversations between educators, practitioners, and researchers, we propose three pillars that must be prioritized to prepare students, researchers, and professionals to take full advantage of the cloud-based EO paradigm and guide future growth.

97 MATHEMATICS AND COMPUTING↗

Tonian Carbonates Record Phosphate-Rich Shallow Seas

The early-middle Neoproterozoic is thought to have witnessed significant perturbations to marine P cycling, in turn facilitating the rise of eukaryote-dominated primary production. However, with few robust constraints on aqueous P concentrations, current understanding of Neoproterozoic P cycling is generally model-dependent. To provide new geochemical constraints, we combined microanalytical data sets with solid-state Nuclear Magnetic Resonance, synchrotron-based X-ray Absorption Near Edge Structure spectroscopy, and micro-X-ray Fluorescence imaging to characterize the speciation and distribution of P in Tonian shallow-water carbonate rocks. These data reflect shallow water phosphate concentrations 10–100× higher than modern systems, supporting the hypothesis that tectonically-driven influxes in P periodically initiated kinetically-controlled CaCO 3 deposition, in turn destabilizing marine carbonate chemistry, climate, and nutrient inventories. Alongside these observations, a new compilation and statistical analysis of mudstone geochemistry data indicates that, in parallel, C org and P burial increased across later Tonian continental margins until becoming decoupled at the close of the Tonian, implicating widespread N-limitation triggered by increasing atmospheric O 2 .

58 GEOSCIENCES↗