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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Scalable implementation of polynomial filtering for density functional theory calculation in PARSEC

In this work, we present an efficient implementation of polynomial filtering methods in PARSEC, a real-space pseudopotential based Kohn–Sham density functional theory solver. The implementation described here improves upon a Chebyshev-filtered subspace iteration algorithm used in the previous version of PARSEC. We present a hybrid polynomial filtering scheme that combines Chebyshev-filtered subspace iteration and a spectrum slicing method that partitions the spectrum into several spectral slices and uses bandpass-filtered subspace iteration to compute approximate eigenpairs within each interior slice simultaneously. We describe a procedure to partition a spectrum and construct polynomial filters. We also discuss a number of practical issues such as the use of appropriate data layouts for carrying out the computation on a two-dimensional process grid and how to achieve good load balance by allocating an appropriate number of process groups to each spectral slice. Numerical examples are presented to demonstrate the effectiveness of the hybrid polynomial filtering method as well as the superior parallel scalability of spectrum slicing in comparison to that of Chebyshev-filtered subspace iteration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Rapid evaluation and quality control of next generation sequencing data with FaQCs

Background: Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform's sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects. Results: Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics. Conclusion: FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SPARTA: High-Level Synthesis of Parallel Multi-Threaded Accelerators

This article presents a methodology for the Synthesis of PARallel multi-Threaded Accelerators (SPARTA) from OpenMP annotated C/C++ specifications. SPARTA extends an open-source HLS tool, enabling the generation of accelerators that provide latency tolerance for irregular memory accesses through multithreading, support fine-grained memory-level parallelism through a hot-potato deflection-based network-on-chip (NoC), support synchronization constructs, and can instantiate memory-side caches. Our approach is based on a custom runtime OpenMP library, providing flexibility and extensibility. Experimental results show high scalability when synthesizing irregular graph kernels. The accelerators generated with our approach are, on average, 2.29x faster than state-of-the-art HLS methodologies.

Design automation↗
DOE OSTI2012

Approximate Weighted Matching On Emerging Manycore and Multithreaded Architectures

Graph matching is a prototypical combinatorial problem with many applications in computer science and scientific computing, but algorithms for computing optimal matchings are challenging to parallelize. Approximate matching algorithms provide an alternate route for parallelization, and in many contexts compute near-optimal matchings for large-scale graphs. We present sharedmemory parallel implementations for computing half-approximate weighted matching on state-of-the-art multicore (Intel Nehalem and AMD Magny-Cours), manycore (Nvidia Tesla and Nvidia Fermi) and massively multithreaded (Cray XMT) platforms. We provide two implementations: the first implementation uses shared work queues, and is suited to all these platforms; the second implementation is based on dataflow principles, and exploits the architectural features of the Cray XMT. Using a carefully chosen dataset that exhibits characteristics from a wide range of real-world applications, we show scalable performance across different platforms. In particular, for one instance of the input, an R-MAT graph (RMAT-G), we show speedups of: about 32 on 48 cores of an AMD Magny-Cours; 7 on 8 cores of Intel Nehalem; 3 on Nvidia Tesla and 10 on Nvidia Fermi relative to one core of Intel Nehalem; and 60 on 128 processors of Cray XMT. We demonstrate good weak and strong scaling for graphs with up to a billion edges using up to 12, 800 threads. Given the breadth of this work, we focus on simplicity and portability of software rather than excessive fine-tuning for each platform. To the best of our knowledge, this is the first such large-scale study of the half-approximate weighted matching problem on shared-memory platforms. Driven by the critical enabling role of combinatorial algorithms such as matching in scientific computing and the emergence of informatics applications, there is a growing demand to support irregular computations on current and future computing platforms. In this context, we evaluate the capability of emerging multithreaded platforms to tolerate latency induced by irregular memory access patterns, and to support fine-grained parallelism via light-weight synchronization mechanisms. By contrasting the architectural features of these platforms against the Cray XMT, which is specifically designed to support irregular memory-intensive applications, we delineate the impact of these choices on performance.

Halappanavar, Mahantesh↗
DOE OSTI2011

Quantum Monte Carlo Endstation for Petascale Computing

The major achievements enabled by QMC Endstation grant include * Performance improvement on clusters of x86 multi-core systems, especially on Cray XT systems * New and improved methods for the wavefunction optimizations * New forms of trial wavefunctions * Implementation of the full application on NVIDIA GPUs using CUDA The scaling studies of QMCPACK on large-scale systems show excellent parallel efficiency up to 216K cores on Jaguarpf (Cray XT5). The GPU implementation shows speedups of 10-15x over the CPU implementation on older generation of x86. We have implemented hybrid OpenMP/MPI scheme in QMC to take advantage of multi-core shared memory processors of petascale systems. Our hybrid scheme has several advantages over the standard MPI-only scheme. * Memory optimized: large read-only data to store one-body orbitals and other shared properties to represent the trial wave function and many-body Hamiltonian can be shared among threads, which reduces the memory footprint of a large-scale problem. * Cache optimized: the data associated with an active Walker are in cache during the compute-intensive drift-diffusion process and the operations on an Walker are optimized for cache reuse. Thread-local objects are used to ensure the data affinity to a thread. * Load balanced: Walkers in an ensemble are evenly distributed among threads and MPI tasks. The two-level parallelism reduces the population imbalance among MPI tasks and reduces the number of point-to-point communications of large messages (serialized objects) for the Walker exchange. * Communication optimized: the communication overhead, especially for the collective operations necessary to determine ET and measure the properties of an ensemble, is significantly lowered by using less MPI tasks. The multiple forms of parallelism afforded by QMC algorithms make them ideal candidates for acceleration in the many-core paradigm. We presented the results of our effort to port the QMCPACK simulation code to the NVIDIA CUDA GPU platform. We restructured the CPU algorithms to express additional parallelism, minimize GPU-CPU communication, and efficiently utilize the GPU memory hierarchy. Using mixed precision on GT200 GPUs and MPI for intercommunication and load balancing, we observe typical full-application speedups of approximately 10x to 15x relative to quad-core Xeon CPUs alone, while reproducing the double-precision CPU results within statistical error. We developed an all-electron quantum Monte Carlo (QMC) method for solids that does not rely on pseudopotentials, and used it to construct a primary ultra-high-pressure calibration based on the equation of state of cubic boron nitride. We computed the static contribution to the free energy with the QMC method and obtained the phonon contribution from density functional theory, yielding a high-accuracy calibration up to 900 GPa usable directly in experiment. We computed the anharmonic Raman frequency shift with QMC simulations as a function of pressure and temperature, allowing optical pressure calibration. In contrast to present experimental approaches, small systematic errors in the theoretical EOS do not increase with pressure, and no extrapolation is needed. This all-electron method is applicable to first-row solids, providing a new reference for ab initio calculations of solids and benchmarks for pseudopotential accuracy. We compared experimental and theoretical results on the momentum distribution and the quasiparticle renormalization factor in sodium. From an x-ray Compton-profile measurement of the valence-electron momentum density, we derived its discontinuity at the Fermi wavevector finding an accurate measure of the renormalization factor that we compared with quantum-Monte-Carlo and G0W0 calculations performed both on crystalline sodium and on the homogeneous electron gas. Our calculated results are in good agreement with the experiment. We have been studying the heat of formation for various Kubas complexes of molecular hydrogen on Ti(1,2)ethylene-nH2 using Diffusion Monte Carlo. This work has been started and is ongoing. We are studying systems involving 1 and 2 Ti bonding sites with up to 10 hydrogen molecules in numerous configurations. This work will establish a benchmark that will test the accuracy of density functional calculations and establish the feasibility of our methods for similar systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Tail queues: A multi-threaded matching architecture

As we approach exascale, computational parallelism will have to drastically increase in order to meet throughput targets. Many–core architectures have exacerbated this problem by trading reduced clock speeds, core complexity, and computation throughput for increasing parallelism. This presents two major challenges for communication libraries such as MPI: the library must leverage the performance advantages of thread level parallelism and avoid the scalability problems associated with increasing the number of processes to that scale. Hybrid programming models, such as MPI+X, have been proposed to address these challenges. MPI THREAD MULTIPLE is MPI's thread safe mode. While there has been work to optimize it, it largely remains non–performant in most implementations. While current applications avoid MPI multithreading due to performance concerns, it is expected to be utilized in future applications. One of the major synchronous data structures required by MPI is the matching engine. In this paper, we present a parallel matching algorithm that can improve MPI matching for multithreaded applications. We then perform a feasibility study to demonstrate the performance benefit of the technique.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Logarithmic Superdiffusion in Two Dimensional Driven Lattice Gases

The spreading of density fluctuations in two-dimensional driven diffusive systems is marginally anomalous. Mode coupling theory predicts that the diffusivity in the direction of the drive diverges with time as (ln t){sup 2/3} with a prefactor depending on the macroscopic current-density relation and the diffusion tensor of the fluctuating hydrodynamic field equation. Here we present the first numerical verification of this behavior for a particular version of the two-dimensional asymmetric exclusion process. Particles jump strictly asymmetrically along one of the lattice directions and symmetrically along the other, and an anisotropy parameter p governs the ratio between the two rates. Using a novel massively parallel coupling algorithm that strongly reduces the fluctuations in the numerical estimate of the two-point correlation function, we are able to accurately determine the exponent of the logarithmic correction. In addition, the variation of the prefactor with p provides a stringent test of mode coupling theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

PetIGA: A framework for high-performance isogeometric analysis

We present PetIGA, a code framework to approximate the solution of partial differential equations using isogeometric analysis. PetIGA can be used to assemble matrices and vectors which come from a Galerkin weak form, discretized with Non-Uniform Rational B-spline basis functions. We base our framework on PETSc, a high-performance library for the scalable solution of partial differential equations, which simplifies the development of large-scale scientific codes, provides a rich environment for prototyping, and separates parallelism from algorithm choice. We describe the implementation of PetIGA, and exemplify its use by solving a model nonlinear problem. To illustrate the robustness and flexibility of PetIGA, we solve some challenging nonlinear partial differential equations that include problems in both solid and fluid mechanics. Lastly, we show strong scaling results on up to 4096 cores, which confirm the suitability of PetIGA for large scale simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Linear scaling pseudo Fermi-operator expansion for fractional occupation

Recursive Fermi-operator expansion methods for the calculation of the idempotent density matrix are valid only at zero electronic temperature with integer occupation numbers. We show how such methods can be modified to include fractional occupation numbers of an approximate or pseudo Fermi-Dirac distribution and how the corresponding entropy term of the free energy is calculated. The proposed methodology is demonstrated and evaluated for different electronic structure methods including density functional tight-binding theory, Kohn-Sham density functional theory using numerical orbitals, and quantum chemistry Hartree-Fock theory using Gaussian basis functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Development of a Reactive Force Field for Simulating Photoinitiated Acrylate Polymerization

Light-driven and photo-curable polymer based additive manufacturing (AM) has enormous potential due to its excellent resolution and precision. Acrylated radical chain-growth polymerized resins are widely used in photopolymer AM due to their fast kinetics, and often serve as a departure point for developing other resin materials for photopolymer-based AM technologies. For successful control of the photopolymer resins, the molecular basis of the acrylate free-radical polymerization has to be understood in detail. We present an optimized reactive force field (ReaxFF) for molecular dynamics (MD) simulations of acrylate polymer resins that captures radical polymerization thermodynamics and kinetics. The force field is trained against an extensive training set including density functional theory (DFT) calculations of reaction pathways along the radical polymerization from methyl acrylate to methyl butyrate, bond dissociation energies, and structures and partial charges of several molecules and radicals. We also found that it was critical to train the force field against an incorrect, nonphysical reaction pathway observed in simulations that used parameters not optimized for acrylate polymerization. As a result, the parameterization process utilizes a parallelized search algorithm, and the resulting model can describe polymer resin formation, crosslinking density, conversion rate, and residual monomers of the complex acrylate mixtures.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Numerical simulation of the dynamics of a liquid crystal in the case of plane strain using GPUs

Parallel computational algorithm is worked out for numerical implementation of two-dimensional dynamic model of a liquid crystal, which takes into account the mutual influence of three physical effects – transfer of acoustic energy due to translational motion, viscoelastic rotation of the particles under the action of tangential stresses, anisotropic thermal expansion and compression. The algorithm is based on the Godunov gap decay method, the Ivanov scheme with controlled dissipation of energy and the splitting method with respect to spatial variables. The CUDA technology for computer systems with graphic accelerators is used. Results of computations demonstrating the efficiency of proposed method and algorithm are represented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Optimization of relativistic backward wave oscillator with non-uniform slow wave structure and a resonant reflector

This letter optimizes synchronously 18 parameters of a relativistic backward wave oscillator with non-uniform slow wave structure (SWS) and a resonant reflector by using the parallel genetic algorithms and particle-in-cell simulation. The optimization results show that the generation efficiency of microwave from the electron beam has increased 32% compared to that of the original device. After optimization, the electromagnetic mode propagating in the resonant changes from the original TM{sub 020} mode of reflector to higher-order TM{sub 021} mode, which has a high reflection coefficient in a broader frequency range than that of the former. The modulation of current inside the optimized device is much deeper than that in the original one. The product of the electric field and current is defined. Observing this product, it is found that the interaction of the electron beam with the electromagnetic wave in the optimized device is much stronger than that in the original device, and at the rear part of SWS of the optimized device, the electron beam dominantly gives out the energy to the electromagnetic wave, leading to the higher generation efficiency of microwave than that of the original device.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Numerical simulation of nonlinear processes in a beam-plasma system

In the present paper we consider the efficiency of the electromagnetic radiation generation due to various nonlinear processes in the beam-plasma system. The beam and plasma parameters were chosen close to the parameters in the experiment on the GOL-3 facility (BINP SB RAS). The model of the collisionless plasma is described by system of the Vlasov-Maxwell equations with periodic boundary conditions. The parallel numerical algorithm is based on the particles-in-cell method (PIC) with mixed Euler-Lagrangian domain decomposition. Various scenarios of nonlinear evolution in the beam-plasma system under the influence of an external magnetic field in case of a low density beam were studied. The energy transfer from one unstable mode to the others modes was observed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗