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At least 1,297 records · Page 72

Efficient Sparse Matrix-Matrix Multiplication on Heterogeneous High Performance Systems

The efficient implementation of sparse matrix-matrix multiplications on high performance parallel machines poses several challenges: large size of input matrices, compressed representation, density of the output matrices, partitioning and load balancing of matrices that present parts with large differences in density and, thus, in computation times. In this paper we show how, starting from the requirements of such application, we developed a framework that allows its efficient implementation on heterogeneous clusters. We introduce a task based programming model and a runtime supported execution model which provides dynamic load balancing on clusters composed by CPUs and GPUs, allowing better utilization of the system while easing the handling of sparse matrices. Our results show that our solution, which co-designs the application together with the programming model and the runtime system, is able to obtain significant speed-ups due to a virtually perfect load balancing with respect to other programming approaches.

97 MATHEMATICS AND COMPUTING↗

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↗

Nonlinear Multiple Models Adaptive Secondary Voltage Control of Microgrids

This article proposes a model-free secondary voltage control (SVC) for microgrids (MG) using nonlinear multiple models adaptive control. Firstly, a linear robust adaptive controller is designed to guarantee the voltage stability in the bounded-input- bounded-output (BIBO) manner so as to meet the operation requirements of MGs. Secondly, a nonlinear adaptive controller is developed to improve the voltage tracking performance with the help of artificial neural networks (ANNs). A switching mechanism for coordinating such two controllers is designed to guarantee the closed-loop stability while achieving accurate voltage tracking. Here, by an online identification based on the input and output data of MGs, the proposed method does not resort to any apriori information of system model and primary control, thus exhibiting good robustness, ease of deployment and disturbance rejection.

17 WIND ENERGY↗

Interaction of intermediate-energy protons with {sup 20}Ne and {sup 24}Mg nuclei within the multiple-scattering model

Observables of the elastic and inelastic scattering of 800- and 250-MeV protons on {sup 20}Ne and {sup 24}Mg nuclei were calculated on the basis of the theory of multiple diffractive scattering and the dispersive {alpha}-cluster model. The {sup 20}Ne and {sup 24}Mg nuclei were assumed to consist of a core ({sup 16}O nucleus) and additional alpha-particle clusters, which could be situated with the highest probability both in the vicinity of the center of mass of the core and outside the core. The multiparticle densities of these nuclei and single-particle nucleon-distribution densities as obtained from the dispersive {alpha}-cluster model were used in the calculations. The differential cross sections and polarizations for elastic and inelastic p{sup 20}Ne and p{sup 24}Mg scattering at the energy of 800 MeV are in better agreement with experimental data than the analogous calculations at the energy of 250 MeV. The spin-rotation functions calculated in the singleparticle approximation for elastic p{sup 20}Ne and p{sup 24}Mg scattering at these two energy values differ qualitatively from their counterparts calculated on the basis of the dispersive {alpha}-cluster model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fission time-scale in experiments and in multiple initiation model

Rate of fission for highly-excited nuclei is affected by the viscose character of the systemmotion in deformation coordinates as was reported for very heavy nuclei with Z{sub C} > 90. The long time-scale of fission can be described in a model of 'fission by diffusion' that includes an assumption of the overdamped diabatic motion. The fission-to-spallation ratio at intermediate proton energy could be influenced by the viscosity, as well. Within a novel approach of the present work, the cross examination of the fission probability, time-scales, and pre-fission neutron multiplicities is resulted in the consistent interpretation of a whole set of the observables. Earlier, different aspects could be reproduced in partial simulations without careful coordination.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Systematics of the mean energy and the mean multiplicity of prompt neutrons originating from {sup 232}Th fission

The cross section for the neutron-induced fission of {sup 232}Th target nuclei, {sigma}{sub f} (E{sub n}), was described within statistical theory. The spectra of the mean multiplicity, v-bar (E{sub n}), and the mean energy, E-bar(E{sub n}), of secondary neutrons accompanying {sup 232}Th fission induced by neutrons of energy extending up to E{sub n} = 20 MeV were analyzed on the basis of the chance structure of the cross section.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Does the multiple-scattering series in the pion-deuteron scattering actually converge?

It is demonstrated that the well-known answer for the multiple-scattering series (MSS) for a light particle interacting to a pair of static nucleons, calculated in the Fixed Centers Approximation (FCA), works well for a wide region of the two-body complex scattering length a. However, this approach is not applicable in a narrow region surrounding the real positive a half-axis, where the MSS does not converge. Simultaneously, for real positive a's the 3-body system forms an infinite set of bound states.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Multiple scattering of elliptically polarized light in two-dimensional medium with large inhomogeneities

For elliptically polarized light incident on a two-dimensional medium with large inhomogeneities, the Stokes parameters of scattered waves are calculated. Multiple scattering is assumed to be sharply anisotropic. The degree of polarization of scattered radiation is shown to be a nonmonotonic function of depth when the incident wave is circularly polarized or its polarization vector is not parallel to the symmetry axis of the inhomogeneities.

74 ATOMIC AND MOLECULAR PHYSICS↗

Charged hadron multiplicities at the HERMES experiment

The HERMES collaboration has measured charge-separated pion and kaon multiplicities in semi-inclusive deep inelastic scattering using a 27.6 GeV electron or positron beam scattering off a hydrogen or deuterium target. The results are presented as a function of the Bjorken variable x {sub B }, the negative squared four-momentum transfer Q {sup 2}, the hadron fractional energy z and it’s transverse momentum P {sub h ⊥}. These data will be very useful to understand the quark-fragmentation process in deep-inelastic hadron electro-production and will serve as crucial input in the understanding of spin asymmetries in polarized semi-inclusive deep-inelastic scattering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

On the Molière theory of multiple scattering of charged particles (1947–1948) and its critique in subsequent years

Several “misconceptions” regarding the theory of multiple scattering of fast charged particles in matter developed by Molière in 1947–1948 and its application in the analysis of experimental results are discussed. It is shown that the critics of this theory misinterpreted the Molière method for determining the cross section of particle scattering by atoms with the screening of their nuclear fields by electron shells described by the Thomas-Fermi statistical model. If the original Molière method is applied consistently, the obtained scattering cross section generally agrees with the results of later classical calculations carried out by Lindhard and his collaborators and other authors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Correlations between multiplicity and transverse momentum in pp, pPb, and Pb–Pb collisions at LHC energies in the dipole-based Monte Carlo string fusion model

Correlations between the multiplicity and transverse momentum in pp, pPb, and Pb–Pb collisions at LHC energies are studied in the framework of the string–parton Monte Carlo model in which elementary collisions are implemented as interactions of color dipoles. The contribution of different mechanisms to the 〈p{sub T}〉{sub N{sub c{sub h}}}−N{sub ch} correlation function is analyzed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

SUSY-Like Relation in Evolution of Gluon and Quark Jet Multiplicities

We show the new relationship [1] between the anomalous dimensions, resummed through next-to-next-to-leading-logarithmic order, in the Dokshitzer–Gribov–Lipatov–Altarelli–Parisi (DGLAP) evolution equations for the first Mellin moments D{sub q,g}(μ{sup 2}) of the quark and gluon fragmentation functions, which correspond to the average hadron multiplicities in jets initiated by quarks and gluons, respectively. This relationship, which is independent of the number of quark flavors, strongly improves previous treatments by allowing for an exact solution of the evolution equations. So far, such relationships have only been known from supersymmetric QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables de novo assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based de novo assembly, including large structural variants and divergent haplotypes. We present NovoGraph, a method for the construction of a human genome graph directly from a set of de novo assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from de novo assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.

59 BASIC BIOLOGICAL SCIENCES↗

Gray Matter Is Targeted in First-Attack Multiple Sclerosis

The cause of multiple sclerosis (MS), its driving pathogenesis at the earliest stages, and what factors allow the first clinical attack to manifest remain unknown. Some imaging studies suggest gray rather than white matter may be involved early, and some postulate this may be predictive of developing MS. Other imaging studies are in conflict. To determine if there was objective molecular evidence of gray matter involvement in early MS we used high-resolution mass spectrometry to identify proteins in the cerebrospinal fluid (CSF) of first-attack MS patients (two independent groups) compared to established relapsing remitting (RR) MS and controls. We found that the CSF proteins in first-attack patients were differentially enriched for gray matter components (axon, neuron, synapse). Myelin components did not distinguish these groups. The results support that gray matter dysfunction is involved early in MS, and also may be integral for the initial clinical presentation.

Environmental Molecular Sciences Laboratory↗

Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass

Genotyping by sequencing allows for large-scale genetic analyses in plant species with no reference genome, but sets the challenge of sound inference in presence of uncertain genotypes. We report an imputation-based genome-wide association study (GWAS) in reed canarygrass (Phalaris arundinacea L., Phalaris caesia Nees), a cool-season grass species with potential as a biofuel crop. Our study involved two linkage populations and an association panel of 590 reed canarygrass genotypes. Plants were assayed for up to 5228 single nucleotide polymorphism markers and 35 traits. The genotypic markers were derived from lowdepth sequencing with 78% missing data on average. To soundly infer marker-trait associations, multiple imputation (MI) was used: several imputes of the marker data were generated to reflect imputation uncertainty and association tests were performed on marker effects across imputes. A total of nine significant markers were identified, three of which showed significant homology with the Brachypodium dystachion genome. Because no physical map of the reed canarygrass genome was available, imputation was conducted using classification trees. In general, MI showed good consistency with the complete-case analysis and adequate control over imputation uncertainty. A gain in significance of marker effects was achieved through MI, but only for rare cases when missing data were ,45%. In addition to providing insight into the genetic basis of important traits in reed canarygrass, this study presents one of the first applications of MI to genome-wide analyses and provides useful guidelines for conducting GWAS based on genotyping-by-sequencing data.

59 BASIC BIOLOGICAL SCIENCES↗

Mountain Basin Controls on the Snow-to-Streamflow Signal: An AIC-Weighted Multiple Linear Regression Framework

A regression-based analysis quantifies how basin characteristics modulate the snow-to-streamflow signal. First, we use the ERA5-Land reanalysis gridded product (European Centre for Medium Range Weather Forecasts reanalysis 5 -Land component) for 4,655 hydrologic unit code - 10 (HUC10) mountain basins across the western United States (US) for water years 1987–2024. Linear regressions are performed for peak snow water equivalent (SWE) and annual streamflow for each mountain basin. Models use ordinary least squares in Python’s statsmodels package. After which, an Akaike Information Criterion (AIC)–weighted ensemble multiple linear regression (MLR) framework with 47 watershed traits is used to predict the linear regression coefficient of determination (r-squared) defining the ability of peak SWE to predict annual streamflow across all mountain basin. Predictor sets are constrained to avoid multicollinearity by excluding models with variance inflation factors (VIF) greater than 5. Mountain basin traits included in the MLR include seasonal climate, topography, vegetation type and structure, and bedrock geology. Accepted models are considered if their AIC is within 2.0 of the model with the minimum AIC, or best model. To compare predictor influence across acceptable models, we computed standardized regression coefficients. To evaluate structural redundancy among models, we constructed binary inclusion vectors for each acceptable model, denoting whether a predictor was present (1) or absent (0). Core predictor variables are defined as occurring in at least 67% of the acceptable models. For this regional analysis, only one model was found acceptable, with higher snow-to-streamflow translation (higher r-squared) occurring in colder mountain basins with higher relative winter precipitation, more snow accumulation and a lower fraction of annual precipitation that falls in the spring and summer. The second component of the data package uses previously published, high-resolution output from an integrated hydrological model of the East River watershed using the U.S. Geological Survey Groundwater and Surface water Flow model (GSFLOW, doi:10.15485/1998576). East River MLR expands upon the approach described above to explore the response of five streamflow metrics—annual streamflow, runoff efficiency, 7-day minimum flow, low-flow duration, and non-perennial stream fraction to snow system indicators including peak SWE, snow-covered area, snow disappearance date, and the fraction of basin area characterized by low-to-no snow, as well as seasonal precipitation and temperature, and annual hydrologic variables representing soil moisture, evapotranspiration (ET), the partitioning of incoming precipitation to evapotranspiration (ET/P), groundwater storage, and groundwater inflow to streams. MLR was done on all water years (P0: 1987-2024) and for each period as determined in the split analysis using pooled regression techniques (P1: 1987-2011 and P2: 2012-2024) to evaluate shifting predictor variable emphasis on streamflow generation. Results indicate that since 2012, peak SWE has lost statistical strength in its prediction of annual streamflow and runoff efficiency, and the indirect influence of spring temperature has emerged as critically important. Low-flow metrics remain largely influenced by soil moisture, vegetation water use and groundwater inflows with summer precipitation becoming a direct influence on minimum summer flow. Together, these data and Python-based analysis tools provide a framework for identifying the key watershed characteristics that control how streamflow responds to snow from year to year. The package also helps quantify uncertainty in statistical models and assess how snow–streamflow relationships vary across regions and over time. This dataset contains comma-separated values files (.csv), text files (.txt), python code files (.py), figure files (.png), and shapefiles (.cpg, .dbf, .prj, .sbn, .sbx, .shp, .xml). Further details on file contents and MLR execution can be found in the readme file and the FLMD files. Work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Multiple Scatters in Single Site Gamma Backgrounds

nEXO aims to reduce its gamma backgrounds by taking advantage of the fact that a large number of gammas that would otherwise be backgrounds will undergo multiple compton scattering in the TPC and produce spatially distinct signals. These multi-sited (MS) events can be excluded from the 0νββ search.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗