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At least 109 records · Page 6

Exploring the interoperability of remote GPGPU virtualization using rCUDA and directive-based programming models

Directive-based programming models, such as OpenMP, OpenACC, and OmpSs, enable users to accelerate applications by using coprocessors with little effort. These devices offer significant computing power, but their use can introduce two problems: an increase in the total cost of ownership and their underutilization because not all codes match their architecture. Remote accelerator virtualization frameworks address those problems. In particular, rCUDA provides transparent access to any graphic processor unit installed in a cluster, reducing the number of accelerators and increasing their utilization ratio. Joining these two technologies, directive-based programming models and rCUDA, is thus highly appealing. In this work, we study the integration of OmpSs and OpenACC with rCUDA, describing and analyzing several applications over three different hardware configurations that include two InfiniBand interconnections and three NVIDIA accelerators. Our evaluation reveals favorable performance results, showing low overhead and similar scaling factors when using remote accelerators instead of local devices.

97 MATHEMATICS AND COMPUTING↗

Extension of frozen natural orbital approximation to open-shell references: Theory, implementation, and application to single-molecule magnets

Natural orbitals are often used to achieve a more compact representation of correlated wave-functions. Using natural orbitals computed as eigenstates of the virtual–virtual block of the state density matrix instead of the canonical Hartree–Fock orbitals results in smaller errors when the same fraction of virtual space is frozen. This strategy, termed frozen natural orbital (FNO) approach, is effective in reducing the cost of regular coupled-cluster (CC) calculations and some multistate methods, such as EOM-IP-CC (equation-of-motion CC for ionization potentials). This contribution extends the FNO approach to the EOM-SF-CC ansatz (EOM-CC with spin-flip). In contrast to EOM-IP-CCSD, EOM-SF-CCSD relies on high-spin open-shell references. Using FNOs computed for an open-shell reference leads to an erratic behavior of the EOM-SF-CC energies and properties due to an inconsistent truncation of the α and β orbital spaces. A general solution to problems arising in the EOM-CC calculations utilizing open-shell references, termed OSFNO (open-shell FNO), is proposed. Furthermore, by means of singular value decomposition (SVD) of the overlap matrix of the α and β orbitals, the OSFNO algorithm identifies the corresponding orbitals and determines virtual orbitals corresponding to the singly occupied space. This is followed by SVD of the singlet part of the state density matrix in the remaining virtual orbital subspace. The so-computed FNOs preserve the spin purity of the open-shell orbital subspace to the extent allowed by the original reference, thus facilitating a safe truncation of the virtual space. The performance of OSFNO is benchmarked for selected diradicals and triradicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SU-E-T-314: The Application of Cloud Computing in Pencil Beam Scanning Proton Therapy Monte Carlo Simulation

Purpose: Monte Carlo simulation plays an important role for proton Pencil Beam Scanning (PBS) technique. However, MC simulation demands high computing power and is limited to few large proton centers that can afford a computer cluster. We study the feasibility of utilizing cloud computing in the MC simulation of PBS beams. Methods: A GATE/GEANT4 based MC simulation software was installed on a commercial cloud computing virtual machine (Linux 64-bits, Amazon EC2). Single spot Integral Depth Dose (IDD) curves and in-air transverse profiles were used to tune the source parameters to simulate an IBA machine. With the use of StarCluster software developed at MIT, a Linux cluster with 2–100 nodes can be conveniently launched in the cloud. A proton PBS plan was then exported to the cloud where the MC simulation was run. Results: The simulated PBS plan has a field size of 10×10cm{sup 2}, 20cm range, 10cm modulation, and contains over 10,000 beam spots. EC2 instance type m1.medium was selected considering the CPU/memory requirement and 40 instances were used to form a Linux cluster. To minimize cost, master node was created with on-demand instance and worker nodes were created with spot-instance. The hourly cost for the 40-node cluster was $0.63 and the projected cost for a 100-node cluster was $1.41. Ten million events were simulated to plot PDD and profile, with each job containing 500k events. The simulation completed within 1 hour and an overall statistical uncertainty of < 2% was achieved. Good agreement between MC simulation and measurement was observed. Conclusion: Cloud computing is a cost-effective and easy to maintain platform to run proton PBS MC simulation. When proton MC packages such as GATE and TOPAS are combined with cloud computing, it will greatly facilitate the pursuing of PBS MC studies, especially for newly established proton centers or individual researchers.

07 ISOTOPE AND RADIATION SOURCES↗

Cepheid Calibration of the Peak Brightness of SNe Ia.: SN 1989B in NGC 3627 - 9

Repeated imaging observations have been made of NGC 3627 with the Hubble Space Telescope in 1997/98, over an interval of 58 days. Images were obtained on 12 epochs in the F555W band and on five epochs in the F8141,V band. The galaxy hosted the prototypical, "Branch normal", type la supernova SN 1989B. A total of 83 variables have been found, of which 68 are definite Cepheid variables with periods ranging from 75 days to 3.85 days. The de-reddened distance modulus is determined to be (m - M)(sub 0) = 30.22 +/- 0.12 (internal uncertainty) using a subset of the Cepheid data whose reddening and error parameters are secure. The photometric data of Wells et al. (1994), combined with the Cepheid data for NGC 3627 give MB(max) = -19.36 +/- 0.18 and M(sub V)(max) = -19.34 +/- 0.16 for SN 1989B. Combined with the previous six calibrations in this program, plus two additional calibrations determined by others gives the mean absolute magnitudes at maximum of (M(sub B)) = -19.48 +/- 0.07 for "Brunch normal" SNe Ia at this interim stage in the calibration program. Using the argument by Wells et al. (1994) that SN 1989B here is virtually identical in decay rate and colors at maximum with SN 198ON in NGC 1316 in the Fornax cluster, and that such identity means nearly identical absolute magnitude, it follows that the difference in the distance modulus of NGC 3627 and NGC 1316 is 1.62 +/- 0.03 mag. Thus the NGC 3627 modulus implies that (m - M)(sub 0) = 31.84 for NGC 1316. The second parameter correlations of M(max) of blue SNe la with decay rate, color at maximum, and Hubble type are re-investigated. The dependence of (M(max)) on decay rate is non-linear, showing a minimum for decay rates between 1.0 less than ADelta(sub m)15 less than 1.6. Magnitudes corrected for decay rate show no dependence on Hubble type, but a dependence on color remains. Correcting both the fiducial sample of 34 SNe la with decay-rate data and the current eight calibrating SNe la for the correlation with decay rate as well as color gives H(sub 0) = 60 +/- 2 (internal) km/s Mpc, in both B and V. The same value to within 4% is obtained if only the SNe la in spirals (without second parameter corrections) are considered. The correlation of SNe la color at maximum with M(max) cannot be due to internal absorption because the slope coefficients in B, V, and I with the change in magnitude are far from or even opposite to the canonical reddening values. The color effect must be intrinsic to the supernova physics. "Absorption" corrections of distant blue SNe la will lead to incorrect values of H(sub 0). The Cepheid distances used in this series are insensitive to metallicity differences. The zeropoint of the P-L relation is based on an assumed LMC modulus of (m - M)(sub 0) = 18.50. As this may have to be increased by 0(sup m).06 to 0(sup m).08, all distances in this paper will follow and Ho will decrease by 3 - 4%.

Saha, A.↗

Linear-Scaling Coupled Cluster with Perturbative Triple Excitations: The Divide–Expand–Consolidate CCSD(T) Model

Here, we propose a reformulation of the traditional (T) triples correction to the coupled cluster singles and doubles (CCSD) energy in terms of local Hartree–Fock (HF) orbitals such that its structural form aligns with our recently developed linear-scaling divide–expand–consolidate (DEC) coupled cluster family of local correlation methods. In a DEC-CCSD(T) calculation, a basis of local occupied and virtual HF orbitals is used to partition the correlated calculation on the full system into a number of independent atomic fragment and pair fragment calculations, each performed within a truncated set of the complete orbital space. In return, this leads to a massively parallel algorithm for the evaluation of the DEC-CCSD(T) correlation energy, which formally scales linearly with the size of the full system and has a tunable precision with respect to a conventional CCSD(T) calculation via a single energy-based input threshold. The theoretical developments are supported by proof of concept DEC-CCSD(T) calculations on a series of medium-sized molecular systems.

Algorithms↗

Effective pairing interaction in a system with an incipient band

The nature and mechanism of superconductivity in the extremely electron-doped FeSe-based superconductors remains an outstanding problem. In these systems, the hole-like band has moved below the Fermi energy, and various spin-fluctuation theories involving pairing between states near the electron Fermi surface and states of this incipient band have been proposed. Using a nonperturbative dynamic cluster quantum Monte Carlo calculation for a bilayer Hubbard model, we show how spin-fluctuation scattering involving intermediate virtual states of the incipient band leads to an effective pairing interaction for the electrons on the remaining Fermi surface. The key feature of this interaction is that it is retarded due to the incipient nature of the hole band and the dynamics of the spin-fluctuation interaction. This allows the pairs to avoid the instantaneous repulsive Coulomb interaction and leads to a frequency dependence of the gap which should be observable in tunneling experiments. Our work provides a different perspective for the pairing mechanism in systems with an incipient band that can be tested in future experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Autonomic Intelligent Cyber Sensor to Support Industrial Control Network Awareness

The proliferation of digital devices in a networked industrial ecosystem, along with an exponential growth in complexity and scope, has resulted in elevated security concerns and management complexity issues. This paper describes a novel architecture utilizing concepts of Autonomic computing and a SOAP based IF-MAP external communication layer to create a network security sensor. This approach simplifies integration of legacy software and supports a secure, scalable, self-managed framework. The contribution of this paper is two-fold: 1) A flexible two level communication layer based on Autonomic computing and Service Oriented Architecture is detailed and 2) Three complementary modules that dynamically reconfigure in response to a changing environment are presented. One module utilizes clustering and fuzzy logic to monitor traffic for abnormal behavior. Another module passively monitors network traffic and deploys deceptive virtual network hosts. These components of the sensor system were implemented in C++ and PERL and utilize a common internal D-Bus communication mechanism. A proof of concept prototype was deployed on a mixed-use test network showing the possible real world applicability. In testing, 45 of the 46 network attached devices were recognized and 10 of the 12 emulated devices were created with specific Operating System and port configurations. Additionally the anomaly detection algorithm achieved a 99.9% recognition rate. All output from the modules were correctly distributed using the common communication structure.

97 MATHEMATICS AND COMPUTING↗

A comparison using APPL and PVM for a parallel implementation of an unstructured grid generation program

Efforts to parallelize the VGRIDSG unstructured surface grid generation program are described. The inherent parallel nature of the grid generation algorithm used in VGRIDSG was exploited on a cluster of Silicon Graphics IRIS 4D workstations using the message passing libraries Application Portable Parallel Library (APPL) and Parallel Virtual Machine (PVM). Comparisons of speed up are presented for generating the surface grid of a unit cube and a Mach 3.0 High Speed Civil Transport. It was concluded that for this application, both APPL and PVM give approximately the same performance, however, APPL is easier to use.

Arthur, Trey↗

A Catalog of Wide Binary and Multiple Systems of Bright Stars from Gaia-DR2 and the Virtual Observatory

Binary and multiple stars have long provided an effective empirical method of testing stellar formation and evolution theories. In particular, the existence of wide binary systems (separations >20,000 au) is particularly challenging to binary formation models as their physical separations are beyond the typical size of a collapsing cloud core (~5000–10,000 au). We mined the recently published Gaia-DR2 catalog to identify bright comoving systems in the five-dimensional space (sky position, parallax, and proper motion). We identified 3741 comoving binary and multiple stellar candidate systems, out of which 575 have compatible radial velocities for all the members of the system. The candidate systems have separations between ~400 and 500,000 au. We used the analysis tools of the Virtual Observatory to characterize the comoving system members and to assess their reliability. The comparison with previous comoving systems catalogs obtained from TGAS showed that these catalogs contain a large number of false systems. In addition, we were not able to confirm the ultra-wide binary population presented in these catalogs. The robustness of our methodology is demonstrated by the identification of well known comoving star clusters and by the low contamination rate for comoving binary systems with projected physical separations <50,000 au. These last constitute a reliable sample for further studies. The catalog is available online at the Spanish Virtual Observatory portal (http://svo2.cab.inta-csic.es/vocats/v2/comovingGaiaDR2/).

79 ASTRONOMY AND ASTROPHYSICS↗

Variational quantum eigensolver for approximate diagonalization of downfolded Hamiltonians using generalized unitary coupled cluster ansatz

In this paper we discuss the utilization of Variational Quantum Solver (VQE) and recently introduced Generalized Unitary Coupled Cluster (GUCC) formalism for the diagonalization of downfolded/effective Hamiltonians in active spaces. In addition to effective Hamiltonians defined by the downfolding of a subset of virtual orbitals we also consider their form defined by freezing core orbitals, which enables us to deal with larger systems. Furthermore, we also consider various solvers to identify solutions of the GUCC equations. We use N 2 , H 2 O, and C 2 H 4 , and benchmark systems to illustrate the performance of the combined framework.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Hardware of Smaller Clusters

Chris Saunders and three technologists are in high demand from Sandia's deep learning teams, and they're kept busy by building new clusters of computer nodes for researchers who need the power of supercomputing on a smaller scale. Sandia researchers working on Laboratory Directed Research & Development (LDRD) projects, or innovative ideas for solutions on short timeframes, formulate new ideas on old themes and frequently rely on smaller cluster machines to help solve problems before introducing their code to larger HPC resources. These research teams need an agile hardware and software environment where nascent ideas can be tested and cultivated on a smaller scale. Saunders and his team at Sandia's Science and Engineering Computing Environments are successfully enabling this research by creating pipelines for emerging code—from Cloud, to containers, to virtual machines—that build the right environment quickly to help teams solve their problems in a matter of days rather than months. While the larger HPC sources are available, it's these smaller clusters that can rapidly build a foundation for teams to build on for later development on larger systems.

97 MATHEMATICS AND COMPUTING↗

Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

We have implemented the polarizable continuum model within the framework of the many-body Green’s function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

H2O/Ni(100) and NH3/Ni(100) - A computational approach

The adsorption of NH3 and H2O on the Ni(100) is treated using a cluster model. The adsorption is found to have only a small effect on the HXH angle. Rotation about the principal ligand axis requires virtually no energy. Ligand tilts of 15 deg are found to require small amounts of energy, leading to the suggestion that the ESDIAD signal is a result of excited tilting modes, not a change in the HXH angle. For H2O additional bending modes are considered and all are found to be quite flat in energy.

Bauschlicher, C. W., Jr.↗

PVM Enhancement for Beowulf Multiple-Processor Nodes

A recent version of the Parallel Virtual Machine (PVM) computer program has been enhanced to enable use of multiple processors in a single node of a Beowulf system (a cluster of personal computers that runs the Linux operating system). A previous version of PVM had been enhanced by addition of a software port, denoted BEOLIN, that enables the incorporation of a Beowulf system into a larger parallel processing system administered by PVM, as though the Beowulf system were a single computer in the larger system. BEOLIN spawns tasks on (that is, automatically assigns tasks to) individual nodes within the cluster. However, BEOLIN does not enable the use of multiple processors in a single node. The present enhancement adds support for a parameter in the PVM command line that enables the user to specify which Internet Protocol host address the code should use in communicating with other Beowulf nodes. This enhancement also provides for the case in which each node in a Beowulf system contains multiple processors. In this case, by making multiple references to a single node, the user can cause the software to spawn multiple tasks on the multiple processors in that node.

Springer, Paul↗

High resolution near-infrared imaging of the trapezium: A stellar census

We present high spatial resolution (0.35 and 0.65 arcsec full width at half maximum (FWHM)) near-infrared images of the central 0.2x0.2 pc of the Trapezium Cluster in the Orion Nebula, centered on the Trapezium OB stars. These images provide the most complete census of stars in this region, and we give accurate positions and near-infrared (2.1 microns) magnitudes for 123 stars. After accounting for line-of-sight projection, we estimate a stellar density for the cluster of approximately 4.7 X 10(exp 4) stars per cubic parsec in the approximately 0.1 pc diameter core. We identify stellar counterparts to virtually all the known dense knots of ionized gas seen at optical and radio wavelengths, strongly supporting the hypothesis that many are either intrinsic stellar radio emitters or circumstellar disks around stars, and not simply dense clumps of gas and dust. We derive approximate masses for the stars associated with the compact knots, finding that the majority are relatively low mass.

Mccaughrean, Mark J.↗

Entrapped Molecule‐Like Europium‐Oxide Clusters in Zinc Oxide with Nearly Unaffected Host Structure

Abstract Nanocrystalline ZnO sponges doped with 5 mol% EuO 1.5 are obtained by heating metal–salt complex based precursor pastes at 200–900 °C for 3 min. X‐ray diffraction, transmission electron microscopy, and extended X‐ray absorption fine structure (EXAFS) show that phase separation into ZnO:Eu and c ‐Eu 2 O 3 takes place upon heating at 700 °C or higher. The unit cell of the clean oxide made at 600 °C shows only ≈0.4% volume increase versus undoped ZnO, and EXAFS shows a ZnO local structure that is little affected by the Eu‐doping and an average Eu 3+ ion coordination number of ≈5.2. Comparisons of 23 density functional theory‐generated structures having differently sized Eu‐oxide clusters embedded in ZnO identify three structures with four or eight Eu atoms as the most energetically favorable. These clusters exhibit the smallest volume increase compared to undoped ZnO and Eu coordination numbers of 5.2–5.5, all in excellent agreement with experimental data. ZnO defect states are crucial for efficient Eu 3+ excitation, while c ‐Eu 2 O 3 phase separation results in loss of the characteristic Eu 3+ photoluminescence. The formation of molecule‐like Eu‐oxide clusters, entrapped in ZnO, proposed here, may help in understanding the nature of the unexpected high doping levels of lanthanide ions in ZnO that occur virtually without significant change in ZnO unit cell dimensions.

36 MATERIALS SCIENCE↗

Structure and Synthesizability of Iron–Sulfur Metal–Organic Frameworks

Sulfur-based metal–organic frameworks (MOFs) and coordination polymers (CPs) are an emerging class of hybrid materials that have received growing attention due to their magnetic, conductive, and catalytic properties with potential applications in electrocatalysis and energy storage. In this work, we report a high-throughput virtual screening protocol to predict the synthesizability of candidate metal–sulfur MOFs/CPs by computing the thermodynamically stable structures resulting from a particular combination of metal cluster, linker, cation, and synthetic conditions. Free energies are computed by using all-atom classical mechanical thermodynamic integration. Low-free-energy structures are refined using ab initio density functional theory, and pair distribution functions and powder X-ray diffraction patterns are calculated to complement and guide experimental structure determination. We validate the computational approach by retrospective predictions of the stable structure produced by experimental syntheses, and a subsequent screen predicts Fe 4 S 4 -BDT–TPP as a new thermodynamically stable one-dimensional (1D) CP comprising a redox-active Fe 4 S 4 cluster, a 1,4-benzenedithiolate (BDT) linker, and a tetraphenylphosphonium (TPP) countercation. Furthermore, this material is experimentally synthesized, and the 1D chain structure of the crystal is confirmed using microcrystal electron diffraction. The computational screening pipeline is generically transferable to neutral and ionic MOFs/CPs comprising arbitrary metal clusters, linkers, cations, and synthetic conditions, and we make it freely available as an open source tool to guide and accelerate the discovery and engineering of novel porous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗