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At least 667 records · Page 37

Single-size and cluster dynamics modeling of intra-granular fission gas bubbles in UO 2

For this work, we perform simulations of intra-granular fission gas bubble evolution in UO 2 using both a relatively simple, computationally inexpensive single-size model and a detailed cluster dynamics model. Simulations encompass 36 experimental cases from 4 different databases, covering various temperature and burnup levels. We systematically compare results from the two models to each other and to post-irradiation experimental data of bubble average size and number density. Overall, the model-to-model comparisons reveal an excellent agreement across the set of simulations. This outcome indicates that, in spite of the underlying assumptions, the single-size model provides a good approximation of the complex physical behavior that is more rigorously described by the cluster dynamics model. Qualitatively, both models reproduce the trends of the experimental data with temperature and burnup correctly. Quantitatively, calculated results are either in good agreement with the data or within errors that appear consistent with the inherent uncertainties. Moreover, for the single-size model, we demonstrate and assess a multiscale approach whereby values for the fission gas atom diffusion coefficient from separate atomistic calculations are used. Systematic comparisons to experimental data point out a credible accuracy of the multiscale model.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A New Technique using Electron Velocity Data from the Four Cluster Spacecraft to Explore Magnetofluid Turbulence in the Solar Wind

It is now possible in certain circumstances to use velocity moments computed from the Plasma Electron and Current Experiment (PEACE) on the four Cluster spacecraft to determine a number of turbulence properties of the solar wind, including direct measurements of the vorticity and compressibility. Assuming that the four spacecraft are not co-planar and that there is only a linear variation of the plasma variables across the volume defined by the four satellites, one can estimate the curl of the fluid velocity, i.e., the vorticity. From the vorticity it is possible to explore directly intermittent regions in the solar wind where dissipation is likely to be enhanced. In addition, one can estimate directly the Taylor microscale.

Goldstein, Melvyn L.↗

Modeling Clustered DNA Damage by Ionizing Radiation Using Multinomial Damage Probabilities and Energy Imparted Spectra

Simple and complex clustered DNA damage represent the critical initial damage caused by radiation. In this paper, a multinomial probability model of clustered damage is developed with probabilities dependent on the energy imparted to DNA and surrounding water molecules. The model consists of four probabilities: (A) direct damage of sugar-phosphate moieties leading to SSB, (B) OH− radical formation with subsequent SSB and BD formation, (C) direct damage to DNA bases, and (D) energy imparted to histone proteins and other molecules in a volume not leading to SSB or BD. These probabilities are augmented by introducing probabilities for the relative location of SSB using a ≤10 bp criteria for a double-strand break (DSB) and for the possible success of a radical attack that leads to SSB or BD. Model predictions for electrons, 4He, and 12C ions are compared to the experimental data and show good agreement. Thus, the developed model allows an accurate and rapid computational method to predict simple and complex clustered DNA damage as a function of radiation quality and to explore the resulting challenges to DNA repair.

Biochemistry & Molecular Biology↗

The SRG/eROSITA All-Sky Survey: Exploring halo assembly bias with X-ray-selected superclusters

Numerical simulations indicate that the clustering of dark matter halos is not only dependent on the halo masses but has a secondary dependence on other properties, such as the assembly history of the halo. This phenomenon, known as the halo assembly bias (HAB), has been found mostly on galaxy scales; observational evidence on larger scales is scarce. In this work, we propose a novel method for exploring HAB on cluster scales using large samples of superclusters. Leveraging the largest-ever X-ray galaxy cluster and supercluster samples obtained from the first SRG/eROSITA all-sky survey, we constructed two subsamples of galaxy clusters that consist of supercluster members and isolated clusters, respectively. After correcting for the selection effects on redshift, mass, and survey depth, we computed the excess in the concentration of the intracluster gas of isolated clusters with respect to supercluster members, defined as δc gas ≡ c gas , ISO /c gas , SC –1 , to investigate the environmental effect on the concentration of clusters, a sign of HAB on cluster scales. We find that the average gas mass concentration of isolated clusters is a few percent higher than that of supercluster members, with a maximum significance of 2.8σ. The result for δc gas varies with the overdensity ratio, f, in supercluster identification, cluster mass proxies, and mass and redshift ranges but remains positive in almost all the measurements. We measure slightly larger δc gas when adopting a higher f for supercluster identification. The δc gas is also higher for low-mass and low-redshift clusters. We performed weak lensing analyses to compare the total mass concentration of the two classes and find a similar trend in total mass concentration as obtained from the gas mass concentration. Our results are consistent with the prediction of HAB on cluster scales, where halos located in denser environments are less concentrated; this trend is stronger for halos with lower masses and at lower redshifts. These phenomena can be explained by the fact that clusters in denser environments, such as superclusters, have experienced more mergers than isolated clusters in their assembling history. This work paves the way to explore HAB with X-ray superclusters and demonstrates that large samples of superclusters with X-ray and weak-lensing data can advance our understanding of the evolution of the large-scale structure.

79 ASTRONOMY AND ASTROPHYSICS↗

aphBO-2GP-3B: a budgeted asynchronous parallel multi-acquisition functions for constrained Bayesian optimization on high-performing computing architecture

High-fidelity complex engineering simulations are often predictive, but also computationally expensive and often require substantial computational efforts. The mitigation of computational burden is usually enabled through parallelism in high-performance cluster (HPC) architecture. Optimization problems associated with these applications is a challenging problem due to the high computational cost of the high-fidelity simulations. In this paper, an asynchronous parallel constrained Bayesian optimization method is proposed to efficiently solve the computationally expensive simulation-based optimization problems on the HPC platform, with a budgeted computational resource, where the maximum number of simulations is a constant. The advantage of this method are three-fold. Firstly, the efficiency of the Bayesian optimization is improved, where multiple input locations are evaluated parallel in an asynchronous manner to accelerate the optimization convergence with respect to physical runtime. This efficiency feature is further improved so that when each of the inputs is finished, another input is queried without waiting for the whole batch to complete. Second, the proposed method can handle both known and unknown constraints. Third, the proposed method samples several acquisition functions based on their rewards using a modified GP-Hedge scheme. The proposed framework is termed aphBO-2GP-3B, which means asynchronous parallel hedge Bayesian optimization with two Gaussian processes and three batches. The numerical performance of the proposed framework aphBO-2GP-3B is comprehensively benchmarked using 16 numerical examples, compared against other 6 parallel Bayesian optimization variants and 1 parallel Monte Carlo as a baseline, and demonstrated using two real-world high-fidelity expensive industrial applications. The first engineering application is based on finite element analysis (FEA) and the second one is based on computational fluid dynamics (CFD) simulations.

97 MATHEMATICS AND COMPUTING↗

Clustering of CODEX clusters

The clustering of galaxy clusters links the spatial nonuniformity of dark matter halos to the growth of the primordial spectrum of perturbations. The amplitude of the clustering signal is widely used to estimate the halo mass of astrophysical objects. The advent of cluster mass calibrations enables using clustering in cosmological studies. Aims. We analyze the autocorrelation function of a large contiguous sample of galaxy clusters, the Constrain Dark Energy with X-ray (CODEX) sample, in which we take particular care of cluster definition. These clusters were X-ray selected using the ROentgen SATellite All-Sky Survey and then identified as galaxy clusters using the code redMaPPer run on the photometry of the Sloan Digital Sky Survey. We develop methods for precisely accounting for the sample selection effects on the clustering and demonstrate their robustness using numerical simulations. Methods. Using the clean CODEX sample, which was obtained by applying a redshift-dependent richness selection, we computed the two-point autocorrelation function of galaxy clusters in the 0.1 < z < 0.3 and 0.3 < z < 0.5 redshift bins. We compared the bias in the measured correlation function with values obtained in numerical simulations using a similar cluster mass range. Results. By fitting a power law, we measured a correlation length r 0 = 18.7 ± 1.1 and slope γ = 1.98 ± 0.14 for the correlation function in the full redshift range. By fixing the other cosmological parameters to their nine-year Wilkinson Microwave Anisotropy Probe values, we reproduced the observed shape of the correlation function under the following cosmological conditions: Ω m0 = $0.22_{-0.03}^{+0.04}$ and S 8 = σ 8 (Ω m0 /0.3)0.5 = $0.85_{-0.08}^{+0.10}$ with estimated additional systematic errors of σ Ω m0 = 0.02 and σS 8 = 0.20. We illustrate the complementarity of clustering constraints by combining them with CODEX cosmological constraints based on the X-ray luminosity function, deriving Ωm = 0.25 ± 0.01 and σ 8 = $0.81_{-0.02}^{+0.01}$ with an estimated additional systematic error of σ Ω m0 = 0.07 and σ σ8 = 0.04. The mass calibration and statistical quality of the mass tracers are the dominant source of uncertainty.

79 ASTRONOMY AND ASTROPHYSICS↗

ICAP: An Interactive Cluster Analysis Procedure for analyzing remotely sensed data

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. The algorithm interfaces the rapid numerical processing capacity of a computer with the human ability to integrate qualitative information. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters and the analyst, who evaluate and elect to modify the cluster structure. Clusters can be deleted or lumped pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The ICAP was implemented in APL (A Programming Language), an interactive computer language. The flexibility of the algorithm was evaluated using data from different LANDSAT scenes to simulate two situations: one in which the analyst is assumed to have no prior knowledge about the data and wishes to have the clusters formed more or less automatically; and the other in which the analyst is assumed to have some knowledge about the data structure and wishes to use that information to closely supervise the clustering process. For comparison, an existing clustering method was also applied to the two data sets.

Wharton, S. W.↗

Predicting Cell Death and Mutation Frequency for a Wide Spectrum of LET by Assuming DNA Break Clustering Inside Repair Domains

Cosmic radiation, which is composed of high charged and energy (HZE) particles, is responsible for cell death and mutation, which may be involved in cancer induction. Mutations are consequences of mis-repaired DNA breaks – especially double-strand breaks (DSBs) – that induce inter- and intra-chromosomal rearrangements (translocations, deletions, inversion). In this study, a computer simulation model is used to investigate the clustering of DSBs in repair domains, previously evidenced by our group in human breast cells [1]. This model is calibrated with experimental data measuring persistent 53BP1 radiation-induced foci (RIF) and is used to explain the high relative biological effectiveness (RBE) of HZE for both cell death and DNA mutation frequencies. We first validate our DSB cluster model using a new track structure model deployed on a simple geometrical configuration for repair domains in the nucleus; then we extend the scope from cell death to mutation induction. This work suggests that mechanism based on DSB repair process can explain several biological effects induced by HZE particles on different type of living cells

Plante, Ianik↗

Predicting cell death and mutation frequency for a wide spectrum of LET and across cell lines from DNA break clustering inside repair domains

Cosmic radiation, which is composed of high charged and energy (HZE) particles, is responsible for cell death and mutation, which may be involved in cancer induction. Mutations are consequences of mis-repaired DNA breaks – especially double-strand breaks (DSBs) – that induce inter- and intra-chromosomal rearrangements (translocations, deletions, inversion). In this study, a computer simulation model is used to investigate the clustering of DSBs in repair domains, previously evidenced by our group in human breast cells. This model is calibrated with experimental data measuring persistent 53BP1 radiation-induced foci (RIF) and is used to explain the high relative biological effectiveness (RBE) of HZE for both cell death and DNA mutation frequencies. We first validate our DSB cluster model using a new track structure model deployed on a simple geometrical configuration for repair domains in the nucleus; then we extend the scope from cell death to mutation induction. This work suggests that mechanism based on DSB repair process can explain several biological effects induced by HZE particles on different type of living cells.

Ianik Plante↗

PluginPlay: Enabling exascale scientific software one module at a time

For many computational chemistry packages, being able to efficiently and effectively scale across an exascale cluster is a heroic feat. Collective experience from the Department of Energy’s Exascale Computing Project suggests that achieving exascale performance requires far more planning, design, and optimization than scaling to petascale. In many cases, entire rewrites of software are necessary to address fundamental algorithmic bottlenecks. This in turn requires a tremendous amount of resources and development time, resources that cannot reasonably be afforded by every computational science project. It thus becomes imperative that computational science transition to a more sustainable paradigm. Key to such a paradigm is modular software. While the importance of modular software is widely recognized, what is perhaps not so widely appreciated is the effort still required to leverage modular software in a sustainable manner. The present manuscript introduces PluginPlay, https://github.com/NWChemEx-Project/PluginPlay, an inversion-of-control framework designed to facilitate developing, maintaining, and sustaining modular scientific software packages. Here this manuscript focuses on the design aspects of PluginPlay and how they specifically influence the performance of the resulting package. Although, PluginPlay serves as the framework for the NWChemEx package, PluginPlay is not tied to NWChemEx or even computational chemistry. We thus anticipate PluginPlay to prove to be a generally useful tool for a number of computational science packages looking to transition to the exascale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-fidelity learning for interatomic potentials: low-level forces and high-level energies are all you need

The promise of machine learning interatomic potentials (MLIPs) has led to an abundance of public quantum mechanical (QM) training datasets. The quality of an MLIP is directly limited by the accuracy of the energies and atomic forces in the training dataset. Unfortunately, most of these datasets are computed with relatively low-accuracy QM methods, e.g. density functional theory with a moderate basis set. Due to the increased computational cost of more accurate QM methods, e.g. coupled-cluster theory with a complete basis set (CBS) extrapolation, most high-accuracy datasets are much smaller and often do not contain atomic forces. The lack of high-accuracy atomic forces is quite troubling, as training with force data greatly improves the stability and quality of the MLIP compared to training to energy alone. Because most datasets are computed with a unique level of theory, traditional single-fidelity (SF) learning is not capable of leveraging the vast amounts of published QM data. In this study, we apply multi-fidelity learning (MFL) to train an MLIP to multiple QM datasets of different levels of accuracy, i.e. levels of fidelity. Specifically, we perform three test cases to demonstrate that MFL with both low-level forces and high-level energies yields an extremely accurate MLIP—far more accurate than a SF MLIP trained solely to high-level energies and almost as accurate as a SF MLIP trained directly to high-level energies and forces. Therefore, MFL greatly alleviates the need for generating large and expensive datasets containing high-accuracy atomic forces and allows for more effective training to existing high-accuracy energy-only datasets. Indeed, low-accuracy atomic forces and high-accuracy energies are all that are needed to achieve a high-accuracy MLIP with MFL.

36 MATERIALS SCIENCE↗

Automated clustering-based workload characterization

The demands placed on the mass storage systems at various federal agencies and national laboratories are continuously increasing in intensity. This forces system managers to constantly monitor the system, evaluate the demand placed on it, and tune it appropriately using either heuristics based on experience or analytic models. Performance models require an accurate workload characterization. This can be a laborious and time consuming process. It became evident from our experience that a tool is necessary to automate the workload characterization process. This paper presents the design and discusses the implementation of a tool for workload characterization of mass storage systems. The main features of the tool discussed here are: (1)Automatic support for peak-period determination. Histograms of system activity are generated and presented to the user for peak-period determination; (2) Automatic clustering analysis. The data collected from the mass storage system logs is clustered using clustering algorithms and tightness measures to limit the number of generated clusters; (3) Reporting of varied file statistics. The tool computes several statistics on file sizes such as average, standard deviation, minimum, maximum, frequency, as well as average transfer time. These statistics are given on a per cluster basis; (4) Portability. The tool can easily be used to characterize the workload in mass storage systems of different vendors. The user needs to specify through a simple log description language how the a specific log should be interpreted. The rest of this paper is organized as follows. Section two presents basic concepts in workload characterization as they apply to mass storage systems. Section three describes clustering algorithms and tightness measures. The following section presents the architecture of the tool. Section five presents some results of workload characterization using the tool.Finally, section six presents some concluding remarks.

Pentakalos, Odysseas I.↗

Galaxy cluster profiles: a Gaussian mixture model approach to halo miscentering

Measurements of the galaxy density and weak-lensing profiles of galaxy clusters typically rely on an assumed cluster center, which is taken to be the brightest cluster galaxy or other proxies for the true halo center defined as the minimum in the potential well. Departure of the assumed cluster center from the true halo center bias the resultant profile measurements, an effect known as miscentering bias. Currently, miscentering is typically modeled in stacked profiles of clusters with a two parameter model. We use an alternate approach in which the profiles of individual clusters are used with the corresponding likelihood computed using a Gaussian mixture model. We test the approach using halos and the corresponding subhalo profiles from the IllustrisTNG hydrodynamic simulations. We obtain significantly improved estimates of the miscentering parameters for both 3D and projected 2D profiles relevant for imaging surveys. We discuss applications to upcoming cosmological surveys. Our Python package for the Gaussian mixture model is publicly available at https://github.com/KyleMiller1/Halo-Miscentering-Mixture-Model.

Bayesian reasoning↗

First-Principles Grand-Canonical Simulations of Water Adsorption in Proton-Exchanged Zeolites

Water appears by design or as impurities in many important reactive systems. For those catalyzed by porous solid acids, such as widely used zeolites, experimentally quantifying the amount or elucidating the structure of adsorbed water clusters at reaction conditions is challenging, while computational studies (e.g., first-principles molecular dynamics simulations) often need to assume the loading to examine solvation effects. Furthermore, we perform first-principles grand-canonical simulations to predict water adsorption to H-ZSM-5 zeolites under specified experimental conditions. Presampling with inexpensive force fields and a pool-based parallelization algorithm are used to improve simulation efficiency, while molecular dynamics is used to sample configurations involving hydronium species. We observe that H + exchange dramatically increases the hydrophilicity of zeolite MFI and an appreciable amount of water is present at very low relative humidities. At all conditions examined, the zeolitic protons are found to dissociate readily from the surface basic sites and become mobile by participating in the hydrogen-bonded chains of adsorbed water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computation of shock wave/target interaction

Computational results of shock waves impinging on targets and the ensuing diffraction flowfield are presented. A number of two-dimensional cases are computed with finite difference techniques. The classical case of a shock wave/cylinder interaction is compared with shock tube data and shows the quality of the computations on a pressure-time plot. Similar results are obtained for a shock wave/rectangular body interaction. Here resolution becomes important and the use of grid clustering techniques tend to show good agreement with experimental data. Computational results are also compared with pressure data resulting from shock impingement experiments for a complicated truck-like geometry. Here of significance are the grid generation and clustering techniques used. For these very complicated bodies, grids are generated by numerically solving a set of elliptic partial differential equations.

Mark, A.↗

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory's (ORNL's) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high performance computing (HPC) needs; and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2019 was a big year as OLCF staff ran five world-class resources (the leadershipclass computers Titan and Summit, the large analysis cluster called Eos, and the massive parallel filesystems called Atlas and Alpine)) and also began power and cooling upgrades for a 2021 exascale system called Frontier. While continuing exceptional operation of Titan, Eos, and Rhea, the OLCF released the Summit supercomputer for production on January 1, 2019. Summit debuted as the most capable and efficient system in its class and has been recognized as the most powerful system in the world for its performance on both the high performance linpack (HPL) and conjugate gradient (HPCG) benchmark applications since June 2018 according to TOP500. Summit represents the culmination of a multiyear effort between the OLCF, IBM, NVIDIA, and Mellanox to deliver a system that is unmatched for modeling, simulation, data analysis, and learning. To hit the ground running with science-ready applications on day one, application teams worked closely with the OLCF through the Center for Accelerated Application Readiness (CAAR) program for years in advance of the Summit deployment. CY 2019 was filled with outstanding results and accomplishments: a very high rating from users on overall satisfaction for the sixth year in a row; a tremendous amount of core-hours delivered to researchers from two leadership-class systems; and success in delivering on the allocation split of roughly 60%, 30%, and 10% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director's Discretionary (DD) programs, respectively (see Operational Performance section). These accomplishments, coupled with the high utilization rates (overall and capability usage), represent the fulfillment of the promise of both leadership-class machines: efficient facilitation of leadership-class computational applications. Table ES.1 presents a summary of the 2019 OLCF metric targets and the associated results. More information can be found in the Operational Performance section for each OLCF resource. The scientific accomplishments of OLCF users are a strong indication of long-term operational success, with publications this year in such notable journals and publications as Nature, Nature Physics, Nature Plants, Physical Review X, Journal of the American Physical Society, Cell, Nano Letters, and Trends in Biotechnology. Crucial domain-specific discoveries facilitated by resources at the OLCF are described in the High Performance Computing Facility Operational Assessment 2019 Oak Ridge Leadership Computing Facility (OAR) Strategic Results section. For example, researchers used Summit to pinpoint and understand the production of proteins from genetic information, including mutations and the functional expression of disease (Section 8.2).

97 MATHEMATICS AND COMPUTING↗

Bridging Aromatic/Antiaromatic Units: Recent Advances in Aromaticity and Antiaromaticity in Main-group and Transition-Metal Clusters from Bonding and Magnetic Analyses

Synthetic exploration and theoretical characterization of metal clusters are actively developing branches of modern inorganic chemistry. Advances in these areas constantly expand the rich structural diversity of viable species, allowing a detailed study of the fundamental characteristics of bench-stable compounds. In this minireview, we summarize recent achievements in synthesis and computational analyses of main-group and heterometallic clusters containing multiple aromatic/antiaromatic units. These systems range from bare clusters to ligand-decorated aggregates, providing a fundamental understanding of the aromaticity and antiaromaticity concepts in species exhibiting unprecedented shapes and composition. The review gives a comprehensive summary of bonding and magnetic response properties of such systems deciphered from the Adaptive Natural Density Partitioning (AdNDP) approach and induced magnetic field analyses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ARENA: Asynchronous Reconfigurable Accelerator Ring to Enable Data-Centric Parallel Computing

The next generation HPC and data centers are likely to be reconfigurable and data-centric due to the trend of hardware specialization and the emergence of data-driven applications. In this work, we propose ARENA – an asynchronous reconfigurable accelerator ring architecture as a potential scenario on how the future HPC and data centers will be like. Despite using the coarse-grained reconfigurable arrays (CGRAs) as the substrate platform, our key contribution is not only the CGRA-cluster design itself, but also the ensemble of a new architecture and programming model that enables asynchronous tasking across a cluster of reconfigurable nodes, so as to bring specialized computation to the data rather than the reverse. We presume distributed data storage without asserting any prior knowledge on the data distribution. Hardware specialization occurs at runtime when a task finds the majority of data it requires are available at the present node. In other words, we dynamically generate specialized CGRA accelerators where the data reside. The asynchronous tasking for bringing computation to data is achieved by circulating the task token, which describes the dataflow graphs to be executed for a task, among the CGRA cluster connected by a fast ring network. Evaluations on a set of HPC and data-driven applications across different domains show that ARENA can provide better parallel scalability with reduced data movement (53.9 percent). Compared with contemporary compute-centric parallel models, ARENA can bring on average 4.37× speedup. The synthesized CGRAs and their task-dispatchers only occupy 2.93mm 2 chip area under 45nm process technology and can run at 800MHz with on average 759.8mW power consumption. ARENA also supports the concurrent execution of multi-applications, offering ideal architectural support for future high-performance parallel computing and data analytics systems.

97 MATHEMATICS AND COMPUTING↗