Search NASA⌕ Search

SEARCH · Search NASA

Results for “Cluster Computing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,117 records · Page 62

CompNanoTox2015: novel perspectives from a European conference on computational nanotoxicology on predictive nanotoxicology

A first European Conference on Computational Nanotoxicology, CompNanoTox, was held in November 2015 in Benahavís, Spain with the objectives to disseminate and integrate results from the European modeling and database projects (NanoPUZZLES, ModENPTox, PreNanoTox, MembraneNanoPart, MODERN, eNanoMapper and EU COST TD1204 MODENA) as well as to create synergies within the European NanoSafety Cluster. This conference was supported by the COST Action TD1204 MODENA on developing computational methods for toxicological risk assessment of engineered nanoparticles and provided a unique opportunity for crossfertilization among complementary disciplines. The efforts to develop and validate computational models crucially depend on high quality experimental data and relevant assays which will be the basis to identify relevant descriptors. The ambitious overarching goal of this conference was to promote predictive nanotoxicology, which can only be achieved by a close collaboration between the computational scientists (e.g. database experts, modeling experts for structure, (eco) toxicological effects, performance and interaction of nanomaterials) and experimentalists from different areas (in particular toxicologists, biologists, chemists and material scientists, among others). The main outcome and new perspectives of this conference are summarized here.

nanoqsar↗

Coupled‐cluster singles, doubles and perturbative triples with density fitting approximation for massively parallel heterogeneous platforms

Abstract A high‐performance implementation of the coupled‐cluster singles, doubles, and perturbative triples [CCSD(T)] is developed in the Massively Parallel Quantum Chemistry program. Novel features include: (1) reduced memory requirements via a density‐fitting (DF) CCSD implementation utilizing distributed lazy evaluation for tensors with more than two unoccupied indices and (2) the ability to utilize efficiently many‐core nodes (Intel Xeon Phi) and heterogeneous nodes with multiple NVIDIA GPUs on each node. All data that are greater than quadratic in the system size are distributed among processes. Excellent strong scaling is observed on distributed‐memory computers equipped with conventional CPUs, Intel Xeon Phi processors, and heterogeneous nodes with multiple NVIDIA GPUs Canonical CCSD(T) energies can be evaluated for systems containing 200 electrons and 1000 basis functions in a few days using a small size commodity cluster, with even larger computations possible on leadership‐class computing resources.

Peng, Chong↗

A Guide to Conquer the Biological Network Era Using Graph Theory

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this article, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns, motifs and models, and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. Finally, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing, clustering, visualization, link prediction, perturbation, and network alignment as well as the current state-of-the-art tools. We expect this review to reach a very broad spectrum of readers varying from experts to beginners while encouraging them to enhance the field further.

59 BASIC BIOLOGICAL SCIENCES↗

A reaction mechanism for plasma electrolysis of AgNO 3 forming silver nanoclusters and nanoparticles

In plasma-driven solution electrolysis (PDSE), gas-phase plasma-produced species interact with an electrolytic solution to produce, for example, nanoparticles. An atmospheric pressure plasma jet (APPJ) directed onto a liquid solution containing a metallic salt will promote reduction of metallic ions in solution, generating metallic clusters that nucleate to form nanoparticles. In this article, results from a computational investigation are discussed of a PDSE process in which a radio-frequency APPJ sustained in helium impinges on a silver nitrate solution, resulting in growth of silver nanoparticles. A reaction mechanism was developed and implemented in a global plasma chemistry model to predict nanoparticle growth. To develop the reaction mechanism, density functional theory was used to generate probable silver growth pathways up to Ag 9 . Neutral clusters larger than Ag 9 were classified as nanoparticles. Kinetic reaction rate coefficients for thermodynamically favorable growth pathways were estimated based on an existing, empirically determined base reaction mechanism for smaller Ag particle interactions. These rates were used in conjunction with diffusion-controlled reaction rate coefficients that were calculated for other Ag species. The role of anions in reduction of Agn ions in forming nanoparticles is also discussed. Oxygen containing impurities or admixtures to the helium, air entrainment into the APPJ, and dissociation of saturated water vapor above the solution can produce additional reactive oxygen species in solution, resulting in the production of anions and O 2 – in particular. For a given molarity, delivering a sufficient fluence of reducing species will produce similar nanoparticle densities and sizes for all applied power levels. In conclusion, comparisons are made to alternate models for nanoparticle formation, including charged nanoparticles and use of direct current plasmas.

36 MATERIALS SCIENCE↗

ON THE DISCREPANCY BETWEEN THEORETICAL AND X-RAY CONCENTRATION-MASS RELATIONS FOR GALAXY CLUSTERS

In the past 15 years, the concentration-mass relation has been investigated diffusely in theoretical studies. On the other hand, only recently has this relation been derived from X-ray observations. When that happened, the results caused a certain level of concern: the X-ray normalizations and slopes were found significantly dissimilar from those predicted by theory. We analyzed 52 galaxy clusters and groups, simulated with different descriptions of the physical processes that affect the baryonic component, with the purpose of determining whether these discrepancies are real or induced by biases in the computation of the concentration parameter or in the determination of the selection function of the cluster sample for which the analysis is carried out. In particular, we investigate how the simulated concentration-mass relation depends (1) on the radial range used to derive the concentration; (2) on the presence of baryons in the simulations, and on the effect of star formation and feedback from supernovae and active galactic nuclei (AGNs). Finally, we evaluate (3) how the results differ when adopting an X-ray approach for the analysis and (4) how the selection function based on X-ray luminosity can impact the results. All effects studied go in the direction of alleviating the discrepancy between observations and simulations, although with different significance: while the choice of the radial range to fit the profiles and the inclusion of the baryonic component play only a minor role, the X-ray approach to reconstruct the mass profiles and the selection of the cluster sample have a strong impact on the resulting concentration-mass relation. Extending the fit to the most central regions or reducing the fitting radius from the virial boundary to the typical X-ray external radius causes an increase of the normalization in radiative simulations by 5%-10%. In the second case, we measure a slope that is up to twice steeper than that derived by using the typical theoretical radial range. Radiative simulations including only supernova feedback produce 30% higher concentrations than the dark matter case. Such a difference is largely reduced when including the effect of AGN feedback. The concentration-mass relation derived from the X-ray synthetic catalog is significantly steeper due to the combination of several different effects, such as environment, dynamical state and dynamical history of the clusters, bias in mass and temperature measurements, and their dependence on the radius and on the mass of the system. Finally, selecting clusters according to their X-ray luminosity produces a net increase in both normalization and slope of the relation, since at fixed mass, the most luminous clusters are also the most concentrated.

79 ASTRONOMY AND ASTROPHYSICS↗

Accelerating DCA++ (Dynamical Cluster Approximation) Scientific Application on the Summit supercomputer

Optimizing scientific applications on today’s accelerator-based high performance computing systems can be challenging, especially when multiple GPUs and CPUs with heterogeneous memories and persistent non-volatile memories are present. An example is Summit, an accelerator-based system at the Oak Ridge Leadership Computing Facility (OLCF) that is rated as the world’s fastest supercomputer to-date. New strategies are thus needed to expose the parallelism in legacy applications, while being amenable to efficient mapping to the underlying architecture.In this paper we discuss our experiences and strategies to port a scientific application, DCA++, to Summit. DCA++ is a highperformance research application that solves quantum manybody problems with a cutting edge quantum cluster algorithm, the dynamical cluster approximation.Our strategies aim to synergize the strengths of the different programming models in the code. These include: (a) streamlining the interactions between the CPU threads and the GPUs, (b) implementing computing kernels on the GPUs and decreasing CPU-GPU memory transfers, (c) allowing asynchronous GPU communications, and (d) increasing compute intensity by combining linear algebraic operations.Full-scale production runs using all 4600 Summit nodes attained a peak performance of 73.5 PFLOPS with a mixed precision implementation.We observed a perfect strong and weak scaling for the quantum Monte Carlo solver in DCA++, while encountering about 2× input/output (I/O) and MPI communication overhead on the time-to-solution for the full machine run. Our hardware agnostic optimizations are designed to alleviate the communication and I/O challenges observed, while improving the compute intensity and obtaining optimal performance on a complex, hybrid architecture like Summit.

Balduzzi, Giovanni↗

Trajectory analysis via a geometric feature space approach

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.

97 MATHEMATICS AND COMPUTING↗

Molecular growth upon ionization of van der Waals clusters containing HCCH and HCN is a pathway to prebiotic molecules

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain N∙∙∙H bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon–carbon and carbon–nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward scalable quantum computations of atomic nuclei

We solve the nuclear two-body and three-body bound states via quantum simulations of pionless effective field theory on a lattice in position space. While the employed lattice remains small, the usage of local Hamiltonians including two- and three-body forces ensures that the number of Pauli terms scales linearly with increasing numbers of lattice sites. We use an adaptive ansatz grown from unitary coupled cluster theory to parametrize the ground states of the deuteron and 3 He, compute their corresponding energies, and analyze the scaling of the required computational resources. Our quantum simulations reproduce exact benchmarks for 2 H and 3 He within 100 keV, requiring at most 30 layers in the ansatz and thus resulting in modest circuit depths. Additionally, we find the number of shots required to reach a given precision scales linearly in the lattice size and more mildly in the system size. Furthermore, based on the agreement with exact benchmarks and mild scaling, we conclude that this can be an efficient, scalable approach for quantum computations of nuclear ground states, particularly to prepare initial states for quantum phase estimation or other filtering algorithms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Data Intensive Computing on Amazon Web Services

The Geophysical Monitoring Program (GMP) has spent the past few years building up the capability to perform data intensive computing using what have been referred to as “big data” tools. These big data tools would be used against massive archives of seismic signals (>300 TB) to conduct research not previously possible. Examples of such tools include Hadoop (HDFS, MapReduce), HBase, Hive, Storm, Spark, Solr, and many more by the day. These tools are useful for performing data analytics on datasets that exceed the resources of traditional analytic approaches. To this end, a research big data cluster (“Cluster A”) was set up as a collaboration between GMP and Livermore Computing (LC).

97 MATHEMATICS AND COMPUTING↗

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene ( nifH ) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. Furthermore, the developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field. IMPORTANCE: Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. Thus, the utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

59 BASIC BIOLOGICAL SCIENCES↗

Probing electronic wave functions of sodium-doped clusters: Dyson orbitals, anisotropy parameters, and ionization cross-sections

We apply high-level ab initio methods to describe the electronic structure of small clusters of ammonia and dimethylether (DME) doped with sodium, which provide a model for solvated electrons. We investigate the effect of the solvent and cluster size on the electronic states. We consider both energies and properties, with a focus on the shape of the electronic wave function and the related experimental observables such as photoelectron angular distributions. The central quantity in modeling photoionization experiments is the Dyson orbital, which describes the difference between the initial N-electron and final (N-1)-electron states of a system. Dyson orbitals enter the expression of the photoelectron matrix element, which determines total and partial photoionization cross-sections. We compute Dyson orbitals for the Na(NH3)n and Na(DME)m clusters using correlated wave functions (obtained with equation-of-motion coupled-cluster model for electron attachment with single and double substitutions) and compare them with more approximate Hartree-Fock and Kohn-Sham orbitals. As a result, we also analyze the effect of correlation and basis sets on the shapes of Dyson orbitals and the experimental observables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The W40 region in the gould belt: An embedded cluster and H II region at the junction of filaments

We present a multiwavelength study of the W40 star-forming region using infrared (IR) observations in the UKIRT JHK bands, Spitzer Infrared Array Camera bands, and Herschel PACS bands, 2.12 μm H{sub 2} narrowband imaging, and radio continuum observations from GMRT (610 and 1280 MHz), in a field of view (FoV) of ∼34' × 40'. Archival Spitzer observations in conjunction with near-IR observations are used to identify 1162 Class II/III and 40 Class I sources in the FoV. The nearest-neighbor stellar surface density analysis shows that the majority of these young stellar objects (YSOs) constitute the embedded cluster centered on the high-mass source IRS 1A South. Some YSOs, predominantly the younger population, are distributed along and trace the filamentary structures at lower stellar surface density. The cluster radius is measured to be 0.44 pc—matching well with the extent of radio emission—with a peak density of 650 pc{sup –2}. The JHK data are used to map the extinction in the region, which is subsequently used to compute the cloud mass—126 M {sub ☉} and 71 M {sub ☉} for the central cluster and the northern IRS 5 region, respectively. H{sub 2} narrowband imaging shows significant emission, which prominently resembles fluorescent emission arising at the borders of dense regions. Radio continuum analysis shows that this region has a blister morphology, with the radio peak coinciding with a protostellar source. Free-free emission spectral energy distribution analysis is used to obtain physical parameters of the overall photoionized region and the IRS 5 sub-region. This multiwavelength scenario is suggestive of star formation having resulted from the merging of multiple filaments to form a hub. Star formation seems to have taken place in two successive epochs, with the first epoch traced by the central cluster and the high-mass star(s)—followed by a second epoch that is spreading into the filaments as uncovered by the Class I sources and even younger protostellar sources along the filaments. The IRS 5 H II region displays indications of swept-up material that has possibly led to the formation of protostars.

79 ASTRONOMY AND ASTROPHYSICS↗

Preparing NERSC users for Cori, a Cray XC40 system with Intel many integrated cores

The newest NERSC supercomputer Cori is a Cray XC40 system consisting of 2,388 Intel Xeon Haswell nodes and 9,688 Intel Xeon-Phi “Knights Landing” (KNL) nodes. Compared to the Xeon-based clusters NERSC users are familiar with, optimal performance on Cori requires consideration of KNL mode settings; process, thread, and memory affinity; fine-grain parallelization; vectorization; and use of the high-bandwidth MCDRAM memory. This paper describes our efforts preparing NERSC users for KNL through the NERSC Exascale Science Application Program, Web documentation, and user training. We discuss how we configured the Cori system for usability and productivity, addressing programming concerns, batch system configurations, and default KNL cluster and memory modes. Here, system usage data, job completion analysis, programming and running jobs issues, and a few successful user stories on KNL are presented.

97 MATHEMATICS AND COMPUTING↗

PULSATING B-TYPE STARS IN THE OPEN CLUSTER NGC 884: FREQUENCIES, MODE IDENTIFICATION, AND ASTEROSEISMOLOGY

Recent progress in the seismic interpretation of field β Cep stars has resulted in improvements of the physical description in the stellar structure and evolution model computations of massive stars. Further asteroseismic constraints can be obtained from studying ensembles of stars in a young open cluster, which all have similar age, distance, and chemical composition. We present an observational asteroseismology study based on the discovery of numerous multi-periodic and mono-periodic B stars in the open cluster NGC 884. We describe a thorough investigation of the pulsational properties of all B-type stars in the cluster. Overall, our detailed frequency analysis resulted in 115 detected frequencies in 65 stars. We found 36 mono-periodic, 16 bi-periodic, 10 tri-periodic, and 2 quadru-periodic stars and one star with nine independent frequencies. We also derived the amplitudes and phases of all detected frequencies in the U, B, V, and I filter, if available. We achieved unambiguous identifications of the mode degree for 12 of the detected frequencies in nine of the pulsators. Imposing the identified degrees and measured frequencies of the radial, dipole, and quadrupole modes of five pulsators led to a seismic cluster age estimate of log (age/yr) = 7.12-7.28 from a comparison with stellar models. Our study is a proof-of-concept for and illustrates the current status of ensemble asteroseismology of a young open cluster.

79 ASTRONOMY AND ASTROPHYSICS↗

Surface-supported cluster catalysis: Ensembles of metastable states run the show

It has recently been demonstrated that the dynamic behaviour of surface-supported nanocluster catalysts in realistic reaction conditions defies conventional models used in catalysis. This opens new doors in catalysis by giving more leverage in catalyst design, but also requires a major revision of the understanding of how dynamic heterogeneous catalytic interfaces operate, as well as of the computational approaches of catalyst modelling, and experimental methods of catalyst characterization. Key aspects of the new paradigm include the collective action of many catalyst states that form a statistical ensemble in reacting conditions, the catalytic activity and selectivity being driven by rare and metastable catalyst states, reaction thermodynamics and kinetics being controlled by different states of the catalyst, broken scaling relationships, non-Arrhenius behaviours, and catalyst dynamic restructuring being an essential part of the reaction mechanism. For computation, this complexity means the departure from the standard DFT calculations of reaction mechanisms on a single catalyst structure. For experiment, it calls for the development of operando characterization tools with the per-site resolution and the ability to find the minority sites that govern the catalytic activity. For catalyst design, the goal becomes the creation of the catalyst state (geometric and electronic) that might not be present in the as-prepared catalyst, but would develop in the reaction conditions and would have the desired activity then. While cluster catalysts are the most dramatic in their dynamic fluxionality, other amorphous interfaces also exhibit some of it, and thus are also subject to similar paradigm revision.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computing the dipole polarizability of Ca 48 with increased precision

Here, we compute the electric dipole polarizability of 48 Ca with an increased precision by including more correlations than in previous studies. Employing the coupled-cluster method we go beyond single and double excitations and include leading-order three-particle-three-hole (3p-3h) excitations for the ground state, excited states, and the similarity-transformed operator. We study electromagnetic sum rules, such as the bremsstrahlung sum rule m 0 and the polarizability sum rule αD using interactions from chiral effective field theory. To gauge the quality of our coupled-cluster approximations we perform several benchmarks with the effective interaction hyperspherical harmonics approach in 4 He and with self consistent Green's function in 16 O. We compute the dipole polarizability of 48 Ca employing the chiral interaction N 2 LO sat and the 1.8/2.0 (EM). We find that the effect of 3p-3h excitations in the ground state is small for 1.8/2.0 (EM) but non-negligible for N 2 LO sat . The addition of these new correlations allows us to improve the precision of our 48 Ca calculations and reconcile the recently reported discrepancy between coupled-cluster results based on these interactions and the experimentally determined αD from proton inelastic scattering in 48 Ca. For the computation of electromagnetic and polarizability sum rules, the inclusion of leading-order 3p-3h excitations in the ground state is important, while it is less so for the excited states and the similarity-transformed dipole operator.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗