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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.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dynamic load balancing with enhanced shared-memory parallelism for particle-in-cell codes

Furthering our understanding of many of today’s interesting problems in plasma physics – including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects – requires large-scale kinetic simulations using particle-in-cell (PIC) codes. However, these simulations are extremely demanding, requiring that contemporary PIC codes be designed to efficiently use a new fleet of exascale computing architectures. To this end, the key issue of parallel load balance across computational nodes must be addressed. We discuss the implementation of dynamic load balancing by dividing the simulation space into many small, self-contained regions or ‘‘tiles,’’ along with shared-memory (e.g., OpenMP) parallelism both over many tiles and within single tiles. The load balancing algorithm can be used with three different topologies, including two space-filling curves. Here, we tested this implementation in the code Osiris and show low overhead and improved scalability with OpenMP thread number on simulations with both uniform load and severe load imbalance. Compared to other load-balancing techniques, our algorithm gives order-of-magnitude improvement in parallel scalability for simulations with severe load imbalance issues.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Implementing a neural network interatomic model with performance portability for emerging exascale architectures

The two main thrusts of computational science are increasingly accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g. neural network potentials, and novel hardware architectures, e.g. GPUs. Current implementations of neural network potentials are orders of magnitude slower than traditional interatomic models and while looming exascale computing offers the ability to run large, accurate simulations with these models, achieving portable performance for MD with new and varied exascale hardware requires rethinking traditional algorithms, using novel data structures, and library solutions. We re-implement a neural network interatomic model in CabanaMD, an MD proxy application, built on libraries developed for performance portability. Our implementation shows significantly improved thread scaling in this complex kernel as compared to a current LAMMPS implementation, across both strong and weak scaling. Our single-source solution enables simulations up to 20 million atoms on a single CPU node and 4 million atoms with improved performance on a single GPU. Furthermore, we also explore parallelism and data layout choices (using flexible data structures called AoSoAs) and their effect on performance, seeing up to ~50% and ~5% improvements in performance on a GPU by choosing the right level of parallelism and data layout respectively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

QTRAJ 1.0: A Lindblad equation solver for heavy-quarkonium dynamics

Here we introduce an open-source package called QTraj that solves the Lindblad equation for heavy-quarkonium dynamics using the quantum trajectories algorithm. The package allows users to simulate the suppression of heavy-quarkonium states using externally-supplied input from 3+1D hydrodynamics simulations. The code uses a split-step pseudo-spectral method for updating the wave-function between jumps, which is implemented using the open-source multi-threaded FFTW3 package. This allows one to have manifestly unitary evolution when using real-valued potentials. In this paper, we provide detailed documentation of QTraj 1.0, installation instructions, and present various tests and benchmarks of the code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Code modernization strategies for short-range non-bonded molecular dynamics simulations

Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. In this paper, we describe our efforts at modernizing the ESPResSo++ simulation package for molecular dynamics by restructuring its particle data layout for efficient memory accesses and applying vectorization techniques to benefit the calculation of short-range non-bonded forces, which results in an overall three times speedup and serves as a baseline for further optimizations. We also implement fine-grained parallelism for multi-core CPUs through HPX, a C++ runtime system which uses lightweight threads and an asynchronous many-task approach to maximize concurrency. Our goal is to evaluate the performance of an HPX-based approach compared to the bulk-synchronous MPI-based implementation. This requires the introduction of an additional layer to the domain decomposition scheme that defines the task granularity. On spatially inhomogeneous systems, which impose a corresponding load-imbalance in traditional MPI-based approaches, we demonstrate that by choosing an optimal task size, the efficient work-stealing mechanisms of HPX can overcome the overhead of communication resulting in an overall 1.4 times speedup compared to the baseline MPI version.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

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↗
DOE OSTI2017

Multisource Rotating Shield Brachytherapy Apparatus for Prostate Cancer

Purpose: Our purpose is to present a novel multisource rotating shield brachytherapy (RSBT) apparatus for the simultaneous precise angular and linear positioning of partially shielded {sup 153}Gd brachytherapy sources in interstitial needles for the treatment of locally advanced prostate cancer. It is designed to lower the dose to nearby healthy tissues, the urethra in particular, relative to conventional high-dose-rate brachytherapy techniques. Methods and Materials: Following needle implantation through the patient template, an angular drive mechanism is docked to the patient template. Each needle is coupled to a multisource afterloader catheter by a connector passing through a shaft. The shafts are rotated about their axes by translating a moving template between 2 stationary templates. The shafts' surfaces and moving template holes are helically threaded with the same pattern such that translation of the moving template causes simultaneous rotation of the shafts. The rotation of each shaft is mechanically transmitted to the catheter-source-shield combination, inside the needles, via several key-keyway pairs. The catheter angles are simultaneously incremented throughout treatment, and only a single 360° rotation of all catheters is needed for a full treatment. For each rotation angle, source depth in each needle is controlled by a multisource afterloader, which is proposed as an array of belt-driven linear actuators, each of which drives a wire that controls catheter depth in a needle. Results: Treatment plans demonstrated that RSBT with the proposed apparatus reduced urethral D{sub 0.1cm{sup 3}} (the minimum dose delivered to the hottest 0.1cm{sup 3} of the urethra) below that of conventional high-dose-rate brachytherapy by 31% for urethral dose gradient volume within 3 mm of the urethra surface. Treatment time to deliver 20 Gy with the proposed multisource RSBT apparatus by use of nineteen 62.4-GBq {sup 153}Gd sources was 122 minutes. Conclusions: The proposed RSBT delivery apparatus enables a mechanically feasible urethra-sparing treatment technique for prostate cancer in a clinically reasonable time frame.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Viscoelastic necking dynamics between attractive microgels

Hypothesis: Microgels can deform and interpenetrate and display colloid/polymer duality. The effective interaction of microgels in the collapsed state is governed by the interplay of polymer–solvent interfacial tension and bulk elasticity. A connecting neck is shown to mediate microgel interaction, but its temporal evolution has not been addressed. Here we hypothesize that the necking dynamics of attractive microgels exhibits liquid-like or solid-like behavior over different time and length scales. Experiments: We simulate the merging and pinching of attractive microgels with different crosslinking densities in explicit solvent using dissipative particle dynamics. The temporal coalescence dynamics of microgels is investigated and compared with simple liquid and polymeric droplets. We model the neck growth on long time scales using Maxwell model of polymer relaxation and compare the theoretical prediction with simulation data. The mechanical strength of the neck is characterized systematically via simulated pinch-off of microgels by steered molecular dynamics. Findings: We evidence a crossover in the coalescence dynamics reflecting the viscoelastic signature of microgels. In contrast to the common knowledge that viscoelastic materials respond elastically on short time scales, the early expansion of the microgel neck exhibits a linear behavior, similar to the viscous coalescence of liquid droplets. However, the late regime with arrested dynamics resembles sintering of solid particles. Through an analytical model relating microgel dynamics to neck growth, we show that the long-term behavior is governed by stress relaxation of the polymers in the neck region and predict an exponential decay in the rate of growth, which agrees favorably with the simulation. Different from coalescence, the thread thinning in microgel breakup primarily highlights its polymeric characteristics.

42 ENGINEERING↗
DOE OSTI2019

Electron channeling contrast imaging investigation of stacking fault pyramids in GaP on Si nucleation layers

Thin gallium phosphide layers were deposited on (0 0 1) Silicon surfaces via organometallic vapor phase epitaxy and characterized by electron channeling contrast imaging (ECCI). Stacking fault pyramids at a density of up to 6 x 10 7 cm -2 were identified in the GaP nucleation layer by varying the diffraction conditions. We show that these defects originate at the GaP/Si interface and propagate on all four {1 1 1} planes. We observed that such stacking fault pyramids interact with the gliding of misfit dislocations during lattice-mismatched growth and enhance the threading dislocation density. The initial pulsing of TEGa and TBP during the nucleation of GaP on Silicon has been found to strongly influence the formation of those pyramidal defects. Changing the number of pulse cycles allowed us to lower their density by two orders of magnitude from 6 x 10 7 cm -2 to 4 x 10 5 cm -2 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Using electron channeling contrast imaging to inform and improve the growth of high-efficiency GaAs solar cells on nanopatterned GaAs substrates

Patterned substrates provide opportunities for reducing the cost of high-efficiency III-V devices by incorporating mechanically weak layers beneficial for substrate reuse (e.g. by spalling). In this work, the functionality of electron channeling contrast imaging (ECCI) as a tool to efficiently understand and mitigate defect formation is exemplified by developing a process in which high-quality III-V material can be grown on nanopatterned GaAs substrates. Reactive ion etching used in the patterning process was found to damage the GaAs substrate surface, leading to the formation of stacking faults in the epitaxial material as observed by ECCI. Etching the patterned substrates in a 1 NH4OH: 1 H2O2: 50 DI H2O solution for 10 s prior to growth removed the substrate surface damage and stacking faults were no longer present. Growth of solar cell device structures initially produced samples with many macroscale flaws creating shunts in the devices, which complicated the assessment of material quality by device measurements. However, ECCI revealed that the epitaxial material surrounding macroscale flaws was free from any crystallographic defects such as stacking faults and threading dislocations. With this knowledge, we focused on refining the patterning process to eliminate the macroscale flaws. Solar cells were then grown on the improved nanopatterned substrates and exhibited device structures with defect densities less than 5 x 105 cm -2 and average conversion efficiency of 24.8%, nearly identical to devices grown on unpatterned epi-ready substrates (25.0%).

14 SOLAR ENERGY↗
DOE OSTI2026

Stacking fault analysis for the early-stages of PVT growth of 4H-SiC crystals

Here, four types of stacking fault formation mechanisms are identified and discussed for early stage PVT growth of 4H-SiC crystals: Type 1: Shockley / double Shockley stacking fault formation inside the facet; Type 2: Stacking fault formation via 2D nucleation; Type 3: Frank + Shockley (S) stacking fault formation due to deflection of threading mixed dislocation (TMD) by macrosteps; Type 4: “Carrot” defect formation related to overgrowth of the terrace formed by separation of 3c/4 and c/4 step risers after deflection of a TMD by vicinal steps. The results help further reduction of defect generation in 4H-SiC substrates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Fast shared-memory streaming multilevel graph partitioning

In this report we show that a fast parallel graph partitioner can benefit many applications by reducing data transfers. The online methods for partitioning graphs have to be fast and they often rely on simple one-pass streaming algorithms, while the offline methods for partitioning graphs contain more involved algorithms and the most successful methods in this category belong to the multilevel approaches. In this work, we assess the feasibility of using streaming graph partitioning algorithms within the multilevel framework. Our end goal is to come up with a fast parallel offline multilevel partitioner that can produce competitive cutsize quality. We rely on a simple but fast and flexible streaming algorithm throughout the entire multilevel framework. This streaming algorithm serves multiple purposes in the partitioning process: a clustering algorithm in the coarsening, an effective algorithm for the initial partitioning, and a fast refinement algorithm in the uncoarsening. Its simple nature also lends itself easily for parallelization. The experiments on various graphs show that our approach is on the average up to 5.1x faster than the multi-threaded MeTiS, which comes at the expense of only 2x worse cutsize.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Laboratory pull-out tests on fully grouted rock bolts and cable bolts: Results and lessons learned

Laboratory pull-out tests were conducted on the following rock bolts and cable bolts: steel rebars, smooth steel bars, fiberglass reinforced polymer threaded bolts, flexible cable bolts, IR5/IN special cable bolts and Mini-cage cable bolts. The diameter of the tested bolts was between 16 mm and 26 mm. The bolts were grouted in a sandstone sample using resin or cement grouts. The tests were conducted under either constant radial stiffness or constant confining pressure boundary conditions applied on the outer surface of the rock sample. In most tests, the rate of displacement was about 0.02 mm/s. The tests were performed using a pull-out bench that allows testing a wide range of parameters. This paper provides an extensive database of laboratory pull-out test results and confirms the influence of the confining pressure and the embedment length on the pull-out response (rock bolts and cable bolts). Furthermore, it also highlights the sensitivity of the results to the operating conditions and to the behavior of the sample as a whole, which cannot be neglected when the test results are used to assess the bolt-grout or the grout–rock interface.

42 ENGINEERING↗
DOE OSTI2023

High-speed friction stir butt welding of 25.4 mm thick 7175-T79 aluminum alloy

This presents the first experimental demonstration of friction stir butt welding of 25.4 mm thick high-strength, precipitate-strengthened 7XXX aluminum alloy at a welding speed above 500 mm/min and penetration depth greater than 10 mm. Tool pin threads that terminate away from the shoulder region, helped mitigate nearby stress concentration during tool traversing, enabling a higher welding speed while avoiding pin fracture near shoulder. Two kinds of welds—one-sided with full penetration of the plate thickness and double-sided with partial penetration of the plate thickness—were conducted. Significant grain refinement (grain size 1.3 ± 0.8 µm) was evident at the junction of double-sided friction stir welding (FSW) compared to other regions of weld-nugget or base material. Cross-weld tensile testing with digital image correlation revealed high local strains at the junction of double-sided FSW before macro-yield. This strain concentration impeded the typical early necking on advancing/retreating sides of FSW joints, improving the yield strength of as-welded double-sided FSW by 20–24% over slow- to medium-speed one-sided FSW. In conclusion, the joint efficiency of as-welded, double-sided high-speed FSW was about 76% with respect to the base material’s ultimate tensile strength.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Benchmarking the Performance of Neuromorphic and Spiking Neural Network Simulators

Software simulators play a critical role in the development of new algorithms and system architectures in any field of engineering. Neuromorphic computing, which has shown potential in building brain-inspired energy-efficient hardware, suffers a slow-down in the development cycle due to a lack of flexible and easy-to-use simulators of either neuromorphic hardware itself or of spiking neural networks (SNNs), the type of neural network computation executed on most neuromorphic systems. While there are several openly available neuromorphic or SNN simulation packages developed by a variety of research groups, they have mostly targeted computational neuroscience simulations, and only a few have targeted small-scale machine learning tasks with SNNs. Evaluations or comparisons of these simulators have often targeted computational neuroscience-style workloads. In this work, we seek to evaluate the performance of several publicly available SNN simulators with respect to non-computational neuroscience workloads, in terms of speed, flexibility, and scalability. We evaluate the performance of the NEST, Brian2, Brian2GeNN, BindsNET and Nengo packages under a common front-end neuromorphic framework. Our evaluation tasks include a variety of different network architectures and workload types to mimic the computation common in different algorithms, including feed-forward network inference, genetic algorithms, and reservoir computing. We also study the scalability of each of these simulators when running on different computing hardware, from single core CPU workstations to multi-node supercomputers. Our results show that the BindsNET simulator has the best speed and scalability for most of the SNN workloads (sparse, dense, and layered SNN architectures) on a single core CPU. However, when comparing the simulators leveraging the GPU capabilities, Brian2GeNN outperforms the others for these workloads in terms of scalability. NEST performs the best for small sparse networks and is also the most flexible simulator in terms of reconfiguration capability NEST shows a speedup of at least 2x compared to the other packages when running evolutionary algorithms for SNNs. The multi-node and multi-thread capabilities of NEST show at least 2x speedup compared to the rest of the simulators (single core CPU or GPU based simulators) for large and sparse networks. We conclude our work by providing a set of recommendations on the suitability of employing these simulators for different tasks and scales of operations. We also present the characteristics for a future generic ideal SNN simulator for different neuromorphic computing workloads.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

CoSyR: A novel beam dynamics code for the modeling of synchrotron radiation effects

The self-consistent nonlinear dynamics of a relativistic charged particle beam interacting with its complete self-fields is a fundamental problem underpinning many of the accelerator design issues in high brightness beam applications, as well as the development of advanced accelerators. Particularly, synchrotron radiation induced effects in a magnetic dispersive beamline element can lead to collective beam instabilities and emittance growth. A novel beam dynamics code is developed based on a Lagrangian method for the calculation of the particles’ radiation near-fields using wavefront/wavelet meshes via the Green’s function of the Maxwell equations. These fields are then interpolated onto a moving mesh for dynamic update of the beam. This method allows radiation co-propagation and self-consistent interaction with the beam in 2D/3D simulations at greatly reduced numerical errors. Multiple levels of parallelisms are inherent in this method and implemented in our code CoSyR to enable at-scale simulations of nonlinear beam dynamics on modern computing platforms using MPI, multi-threading, and GPUs. Here, the current 2D implementation of CoSyR has been used to evaluate the transverse and longitudinal coherent radiation effects on the beam and to investigate beam optics designs proposed for mitigation of beam brightness degradation in a magnetic bunch compressor. In this paper, the design of CoSyR, as well as the benchmark with other coherent synchrotron radiation models, are described and discussed. Extension of the core algorithms to 3D is possible and planned.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Performance optimization, modeling and analysis of sparse matrix-matrix products on multi-core and many-core processors

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. In this work, we firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We examine their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. We build the performance model for hash-table and heap-based algorithms, which supports the recipe. A critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix. Finally, we integrate our implementations into a large-scale protein clustering code named HipMCL, accelerating its SpGEMM kernel by up to 10X and achieving an overall performance boost for the whole HipMCL application by 2.6X.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin

Tropical forests are acknowledged to be the largest global source of isoprene (C 5 H 8 ) and monoterpenes (C 10 H 16 ) emissions, with current synthesis studies suggesting few tropical species emit isoprenoids (20-38%) and do so with highly variable emission capacities, including within the same genera. This apparent lack of a clear phylogenetic thread has created difficulties both in linking isoprenoid function with evolution and for the development of accurate biosphere-atmosphere models. In this work, we present a systematic emission study of "hyperdominant" tree species in the Amazon Basin. Across 162 individuals, distributed among 25 botanical families and 113 species, isoprenoid emissions were widespread among both early and late successional species (isoprene: 61.9% of the species; monoterpenes: 15.0%; both isoprene and monoterpenes: 9.7%). The hyperdominant species (69) across the top five most abundant genera, which make up about 50% of all individuals in the Basin, had a similar abundance of isoprenoid emitters (isoprene: 63.8%; monoterpenes: 17.4%; both 11.6%). Among the abundant genera, only Pouteria had a low frequency of isoprene emitting species (15.8% of 19 species). In contrast, Protium, Licania, Inga, and Eschweilera were rich in isoprene emitting species (83.3% of 12 species, 61.1% of 18 species, 100% of 8 species, and 100% of 12 species, respectively). Light response curves of individuals in each of the five genera showed light-dependent, photosynthesis-linked emission rates of isoprene and monoterpenes. Importantly, in every genus, we observed species with light-dependent isoprene emissions together with monoterpenes including β-ocimene. These observations support the emerging view of the evolution of isoprene synthases from β-ocimene synthases. Our results have important implications for understanding isoprenoid function-evolution relationships and the development of more accurate Earth System Models.

59 BASIC BIOLOGICAL SCIENCES↗