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At least 1,063 records · Page 59

Applications Performance Under MPL and MPI on NAS IBM SP2

On July 5, 1994, an IBM Scalable POWER parallel System (IBM SP2) with 64 nodes, was installed at the Numerical Aerodynamic Simulation (NAS) Facility Each node of NAS IBM SP2 is a "wide node" consisting of a RISC 6000/590 workstation module with a clock of 66.5 MHz which can perform four floating point operations per clock with a peak performance of 266 Mflop/s. By the end of 1994, 64 nodes of IBM SP2 will be upgraded to 160 nodes with a peak performance of 42.5 Gflop/s. An overview of the IBM SP2 hardware is presented. The basic understanding of architectural details of RS 6000/590 will help application scientists the porting, optimizing, and tuning of codes from other machines such as the CRAY C90 and the Paragon to the NAS SP2. Optimization techniques such as quad-word loading, effective utilization of two floating point units, and data cache optimization of RS 6000/590 is illustrated, with examples giving performance gains at each optimization step. The conversion of codes using Intel's message passing library NX to codes using native Message Passing Library (MPL) and the Message Passing Interface (NMI) library available on the IBM SP2 is illustrated. In particular, we will present the performance of Fast Fourier Transform (FFT) kernel from NAS Parallel Benchmarks (NPB) under MPL and MPI. We have also optimized some of Fortran BLAS 2 and BLAS 3 routines, e.g., the optimized Fortran DAXPY runs at 175 Mflop/s and optimized Fortran DGEMM runs at 230 Mflop/s per node. The performance of the NPB (Class B) on the IBM SP2 is compared with the CRAY C90, Intel Paragon, TMC CM-5E, and the CRAY T3D.

Saini, Subhash↗

Using GANs to predict milling stability from limited data

Milling is a key manufacturing process that requires the selection of operating parameters that provide efficient performance. However, the presence of chatter, a self-excited vibration causing poor surface finish and potential damage to the machine and cutting tool, makes it challenging to select the appropriate parameters. To predict chatter, stability maps are commonly used, but their generation requires expensive data, making it difficult to employ these maps in industry. Therefore, there is a pressing need for an approach that can accurately predict stability maps using limited experimental data. This study introduces the new Encoder GAN (EGAN) approach based on Generative Adversarial Networks (GANs) that predicts stability maps using limited experimental data. The approach consists of the encoder, generator, and discriminator subnetworks and uses the trained encoder and generator to predict the target stability map. This versatile method can be applied to various tool setups and can accurately predict stability maps with limited experimental data (five to 10 cutting tests) even when there is little information available for unknown parameters. In conclusion, the study evaluates the proposed approach using both numerical data and experiments and demonstrates its superior performance compared to state-of-the-art benchmarks.

42 ENGINEERING↗

New bipolar host materials for high power efficiency green thermally activated delayed fluorescence $\mathrm{OLEDs}$

We report four bipolar molecules, namely m-CzPym, p-CzPym, m-CzTrz, and p-CzTrz, with carbazole (Cz) donor and a benzonitrile-substituted pyrimidine (Pym) or triazine (Trz) acceptor core were synthesized and characterized. The electron deficiency of heteroaryl cores together with the substitution pattern of benzonitrile were employed to tune the energy levels as well as the thermally activated delayed fluorescence (TADF) characteristics. The four molecules exhibited TADF behavior with inferior photoluminescent quantum yields (PLQYs) that limit their applications as emitters. These bipolar molecules were employed as TADF host materials for the benchmark TADF emitter 4CzIPN to achieve high-performing green TADF organic light-emitting diodes (OLEDs). Among the molecules, m-CzPym-hosted TADF-OLEDs achieved a maximum external quantum efficiency (EQE max ) of 31.5%, maximum power efficiency (PE max ) of 95.6 lm/W, and maximum current efficiency (CE max ) of 100.2 cd/A. Notably, p-CzPym-hosted TADF-OLEDs also achieved a PE max of 116.5 lm/W, turn-on voltage of 2.5 V, and impressive low efficiency roll-off performance (>89% of EQE max at 5000 cd/m 2 ), representing one of the highest efficiencies ever reported in 4CzIPN-doped devices. The high device efficiency can be ascribed to the balanced ambipolar carrier-transporting character of the host materials and high PLQY as well as the outstanding light outcoupling efficiency of the emitting layer.

42 ENGINEERING↗

HTR solver: An open-source exascale-oriented task-based multi-GPU high-order code for hypersonic aerothermodynamics

In this study, the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics is described. The physical formulation of the code includes thermochemical effects induced by high temperatures (vibrational excitation and chemical dissociation). The HTR solver uses high-order TENO-based spatial discretization on structured grids and efficient time integrators for stiff systems, is highly scalable in GPU-based supercomputers as a result of its implementation in the Regent/Legion stack, and is designed for direct numerical simulations of canonical hypersonic flows at high Reynolds numbers. Additionally, the performance of the HTR solver is tested with benchmark cases including inviscid vortex advection, low- and high-speed laminar boundary layers, inviscid one-dimensional compressible flows in shock tubes, supersonic turbulent channel flows, and hypersonic transitional boundary layers of both calorically perfect gases and dissociating air.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

TTDFT: A GPU accelerated Tucker tensor DFT code for large-scale Kohn-Sham DFT calculations

We present the Tucker tensor DFT (TTDFT) code which uses a tensor-structured algorithm with graphic processing unit (GPU) acceleration for conducting ground-state DFT calculations on large-scale systems. The Tucker tensor DFT algorithm uses a localized Tucker tensor basis computed from an additive separable approximation to the Kohn-Sham Hamiltonian. The discrete Kohn-Sham problem is solved using Chebyshev filtered subspace iteration method that relies on matrix-matrix multiplications of a sparse symmetric Hamiltonian matrix and a dense wavefunction matrix, expressed in the localized Tucker tensor basis. These matrix-matrix multiplication operations, which constitute the most computationally intensive step of the solution procedure, are GPU accelerated providing ~8-fold GPU-CPU speedup for these operations on the largest systems studied. In conclusion, the computational performance of the TTDFT code is presented using benchmark studies on aluminum nano-particles and silicon quantum dots with system sizes ranging up to ~7,000 atoms.

97 MATHEMATICS AND COMPUTING↗

Computing material volume fractions on a superimposed mesh as applied to Monte Carlo particle transport simulations

Here, we present a newly implemented ray tracing algorithm in OpenMC for efficiently computing material volume fractions on superimposed meshes in complex geometries. By firing rays along each coordinate direction through the geometry, the approach accumulates track-length data in each mesh element, thereby determining the fractional composition of each material. Scaling studies on three different models—a random tetrahedra configuration, the Frascati Neutron Generator ITER dose rate benchmark, and a stellarator design—show excellent parallel performance, with nearly linear speedup on modern multi-threaded and distributed-memory systems. An analysis of the residual error relative to high-resolution reference solutions demonstrated that under optimal conditions it decreases as 1/R, where R is the number of rays fired, making it straightforward to achieve user-prescribed accuracy. This new functionality enables practical, mesh-based approaches for detailed nuclear analyses in production Monte Carlo workflows without resorting to expensive, fully conformal or unstructured meshing.

Monte Carlo↗

A high-order Shifted Interface Method for Lagrangian shock hydrodynamics

Here, we present a new method for two-material Lagrangian hydrodynamics, which combines the Shifted Interface Method (SIM) with a high-order Finite Element Method. Our approach relies on an exact (or sharp) material interface representation, that is, it uses the precise location of the material interface. The interface is represented by the zero level-set of a continuous high-order finite element function that moves with the material velocity. This strategy allows to evolve curved material interfaces inside curved elements. By reformulating the original interface problem over a surrogate (approximate) interface, located in proximity of the true interface, the SIM avoids cut cells and the associated problematic issues regarding implementation, numerical stability, and matrix conditioning. Accuracy is maintained by modifying the original interface conditions using Taylor expansions. We demonstrate the performance of the proposed algorithms on established numerical benchmarks in one, two and three dimensions.

97 MATHEMATICS AND COMPUTING↗

Numerical implementation of the MOOSE subchannel module (SCM) algorithm

The subchannel module of moose (SCM), previously referred to as Pronghorn-SC, is a subchannel code designed to resolve single-phase flow fields and calculate the relevant flow variables, in nuclear reactor fuel-pin assemblies. The assemblies it models are: water-cooled, with bare fuel-pins in a square ducted, quadrilateral lattice and liquid-metal/water-cooled, with bare/wire-wrapped fuel pins in a hexagonal ducted, triangular lattice. Previous publications have presented the development, validation and verification of SCM. This work presents an comparative overview of the different solvers implemented within SCM. This includes the solver algorithm description, and a performance comparison. The two test cases chosen to demonstrate the solver performance were taken from the PSBT enthalpy mixing benchmark and the ORNL-19 pin benchmark.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Design Principles for the Synthesis of Self-Pillared ZSM-5 Zeolite Nanosheets

The design of next-generation materials for emerging energy and environmental applications heavily relies on empirical approaches to direct nonclassical nucleation and crystal growth pathways, polymorphism, intercrystalline transformations, and seed-assisted growth processes. A long-standing obstacle to nanoporous materials design is the complexity of their crystallization, which hinders the development of predictive models and/or physical descriptors that can guide their synthesis. In this study, we use a combination of state-of-the-art synthesis, characterization, and computational design to prepare hierarchical MFI-type zeolites, which we couple with benchmark catalytic testing to assess structure-property-performance relationships. These hierarchical materials are intergrowths of two commercially relevant zeolite frameworks, MFI and MEL, prepared as self-pillared pentasil (SPP) zeolites through seed-assisted, organic-free syntheses for which little theoretical guidance existed. Here, by comparing a large library of zeolite seeds with different pore sizes, dimensions, and structural composite building units, we determined the relative impact of seed and silica source selection, among other synthesis variables. Combined experimental and computational studies are used to test several hypotheses in literature to rationalize the choice of seed structure and establish a more robust selection criteria for seed-assisted synthesis of zeolites. Specifically, we show that a data-driven approach to develop structural descriptors correlates to new, facile routes to rationally design SPP zeolites, addressing knowledge gaps in the fundamental understanding of (non)classical crystal growth mechanisms that are characteristic of nanoporous aluminosilicates.

36 MATERIALS SCIENCE↗

Ab initio and force field molecular dynamics study of bulk organophosphorus and organochlorine liquid structures

Here, we performed ab initio molecular dynamics (AIMD) simulations to benchmark bulk liquid structures and to evaluate results from all-atom force field molecular dynamics (FFMD) simulations with the generalized Amber force field (GAFF) for organophosphorus (OP) and organochlorine (OC) compounds. Our work also addresses the current and important topic of force field validation, applied here to a set of nonaqueous organic liquids. Our approach differs from standard treatments, which validate force fields based on thermodynamic data. Utilizing radial distribution functions (RDFs), our results show that GAFF reproduces the AIMD-predicted asymmetric liquid structures moderately well for OP compounds that contain bulky alkyl groups. Among the OCs, RDFs obtained from FFMD overlap well with AIMD results, with some offsets in position and peak structuring. However, re-parameterization of GAFF for some OCs is needed to reproduce fully the liquid structures predicted by AIMD. The offsets between AIMD and FFMD peak positions suggest inconsistencies in the developed force fields, but, in general, GAFF is able to capture short-ranged and long-ranged interactions of OPs and OCs observed in AIMD. Along with the local coordination structure, we also compared enthalpies of vaporization. Overall, calculated bulk properties from FFMD compared reasonably well with experimental values, suggesting that small improvements within the FF should focus on parameters that adjust the bulk liquid structures of these compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The development of a high-resolution Eulerian radiation-hydrodynamics simulation capability for laser-driven Hohlraums

Hohlraums are hollow cylindrical cavities with high-Z material walls used to convert laser energy into uniform x-ray radiation drives for inertial confinement fusion capsule implosions and high energy density physics experiments. Credible computational modeling of hohlraums requires detailed modeling and coupling of laser physics, hydrodynamics, radiation transport, heat transport, and atomic physics. We report on improvements to Los Alamos National Laboratory's xRAGE radiation-hydrodynamics code in order to enable hohlraum modeling. xRAGE's Eulerian hydrodynamics and adaptive mesh refinement make it uniquely well suited to study the impacts of multiscale features in hohlraums. In order to provide confidence in this new modeling capability, we demonstrate xRAGE's ability to produce reasonable agreement with data from several benchmark hohlraum experiments. We also use xRAGE to perform integrated simulations of a recent layered high density carbon capsule implosion on the National Ignition Facility in order to evaluate the potential impacts of the capsule support tent, mixed cell conductivity methodologies, plasma transport, and cross-beam energy transfer (XBT). We find that XBT, seeded by plasma flows in the laser entrance hole (LEH), causes a slight decrease in energy coupling to the capsule and that all of these impact the symmetry of the x-ray drive such that they have an appreciable impact on the capsule implosion shape.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗

Improving deep learning-based protein distance prediction in CASP14

Abstract Motivation Accurate prediction of residue–residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Results Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions [i.e. classifying distances between two residues into two categories: in contact (<8 Angstrom) and not in contact otherwise] and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the precision of distance classification. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps. Availability and implementation The software package, source code and data of DeepDist2 are freely available at https://github.com/multicom-toolbox/deepdist and https://zenodo.org/record/4712084#.YIIM13VKhQM. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Selective electron-phonon coupling strength from nonequilibrium optical spectroscopy: The case of MgB 2

The coupling between quasiparticles and bosonic excitations rules the energy transfer pathways in condensed matter systems. The possibility of inferring the strength of specific coupling channels from their characteristic timescales measured in nonequilibrium experiments is still an open question. Here, in this study, we investigate MgB 2 , in which conventional superconductivity at temperatures as high as 39 K is mediated by the strong coupling between the conduction electrons and the 𝐸 2⁢𝑔 phonon mode. By means of broadband time-resolved optical spectroscopy, we show that this selective electron-phonon coupling dictates the nonequilibrium optical response of MgB 2 at early times (<100 fs) after photoexcitation. Furthermore, based on an effective temperature model analysis, we estimate its contribution to the total electron-boson coupling function extracted from complementary equilibrium spectroscopy approaches, namely, optical reflectivity and angle-resolved photoemission spectroscopy. The coupling strength with the 𝐸 2⁢𝑔 phonon modes is thus estimated to be 𝜆 ≃ 0.56, which is approximately half of the total coupling constant, in agreement with 𝑎𝑏 initio calculations from the literature. As a benchmark, broadband time-resolved optical spectroscopy is performed also on the isostructural and nonsuperconducting compound AlB 2 , showing that the nonequilibrium optical response relaxes on a slower timescale due to the lack of strongly coupled phonon modes. Our findings demonstrate the possibility to resolve and quantify selective electron-phonon coupling from nonequilibrium optical spectroscopy.

Mor, Selene [Università Cattolica del Sacro Cuore,↗

Syncopated dynamical decoupling to suppress crosstalk in quantum circuits

Theoretically understanding and experimentally characterizing and modifying the underlying Hamiltonian of a quantum system is of utmost importance in achieving high-fidelity quantum gates for quantum computing. Here, in this work, we explore the use of dynamical decoupling (DD) in characterizing and suppressing undesired two-qubit couplings as well as the underlying single-qubit decoherence, both significant hurdles to achieving precise quantum control and realizing quantum computing on many hardware prototypes. Through discrete search of DD sequences, we identify sequences that protect against decoherence and selectively target unwanted two-qubit interactions of general form. On a transmon-qubit-based superconducting quantum device, we identify separate white and 1/𝑓 noise components underlying the single-qubit decoherence and a static ZZ coupling between pairs of qubits. A family of syncopated DD sequences is found and their efficiency is demonstrated in two-qubit benchmarking experiments. The syncopated decoupling technique significantly boosts performance in a realistic algorithmic quantum circuit.

97 MATHEMATICS AND COMPUTING↗

Coulomb sum rule for 4 He and 16 O from coupled-cluster theory

We demonstrate the capability of coupled-cluster theory to compute the Coulomb sum rule for the 4 He and 16 O nuclei using interactions from chiral effective field theory. We perform several checks, including a few-body benchmark for 4He. We provide an analysis of the center-of-mass contaminations, which we are able to safely remove. We then compare with other theoretical results and experimental data available in the literature, obtaining a fair agreement. This is a first and necessary step towards initiating a program for computing neutrino-nucleus interactions from first principles in coupled-cluster theory and supporting the experimental long-baseline neutrino program with a state-of-the-art theory that can reach medium-mass nuclei.

6 ≤ A ≤ 19A ≤ 5↗

Probing New Bosons and Nuclear Structure with Ytterbium Isotope Shifts

In this Letter, we present mass-ratio measurements on highly charged Yb 42+ ions with a precision of 4 ×10 -12 and isotope-shift measurements on Yb + on the 2 S 1/2 → 2 D 5/2 and 2 S 1/2 → 2 F 7/2 transitions with a precision of 4 ×10 -9 for the isotopes 168,170,172,174,176 Yb. We present a new method that allows us to extract higher-order changes in the nuclear charge distribution along the Yb isotope chain, benchmarking ab initio nuclear structure calculations. Additionally, we perform a King plot analysis to set bounds on a fifth force in the keV/c 2 to MeV/c 2 range coupling to electrons and neutrons.

74 ATOMIC AND MOLECULAR PHYSICS↗

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi- center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), im- age preprocessing (97%), data curation (79%), and post- processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Eisenmann, Matthias↗