Exa-Graph/vite
MPI+OpenMP implementation of Louvain method for Graph Community Detection, with a number of parallel heuristics/approximate computing techniques Also called "CuVite"
Ghosh, Sayan↗
SEARCH · Engineering Papers
Results for “parallel methods”
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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DIVA/DeviceEditor v6.1.2
DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.
Plahar, Hector [Lawrence Berkeley National Laborat↗
Scalable Second Order Optimization for Machine Learning
Many machine learning (ML) training tasks are essentially optimization processes that would at first glance appear eminently parallelizable and scalable. However, effective acceleration of these tasks with scalable parallel hardware has proven to be elusive. While standard methods for machine learning, e.g., stochastic gradient descent (SGD) for DNNs, tend to be resource efficient, they appear to be fundamentally sequential in nature.
97 MATHEMATICS AND COMPUTING↗
Machine Committee Framework for Power Grid Disturbances Analysis Using Synchrophasors Data
Events detection is a key challenge in power grid frequency disturbances analysis. Accurate detection of events is crucial for situational awareness of the power system. In this paper, we study the problem of events detection in power grid frequency disturbance analysis using synchrophasors data streams. Current events detection approaches for power grid rely on individual detection algorithm. This study integrates some of the existing detection algorithms using the concept of machine committee to develop improved detection approaches for grid disturbance analysis. Specifically, we propose two algorithms—an Event Detection Machine Committee (EDMC) algorithm and a Change-Point Detection Machine Committee (CPDMC) algorithm. Both algorithms use parallel architecture to fuse detection knowledge of its individual methods to arrive at an overall output. The EDMC algorithm combines five individual event detection methods, while the CPDMC algorithm combines two change-point detection methods. Each method performs the detection task separately. The overall output of each algorithm is then computed using a voting strategy. The proposed algorithms are evaluated using three case studies of actual power grid disturbances. Compared with the individual results of the various detection methods, we found that the EDMC algorithm is a better fit for analyzing synchrophasors data; it improves the detection accuracy; and it is suitable for practical scenarios.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Fast and sensitive measurements of sub-3 nm particles using Condensation Particle Counters For Atmospheric Rapid Measurements (CPC FARM)
New particle formation (NPF) is the atmospheric process whereby gas molecules react and nucleate to form detectable particles. NPF has a strong impact on Earth's radiative balance as it produces roughly half of global cloud condensation nuclei. However, the time resolution and sensitivity of current instrumentation are inadequate in measuring the size distribution of sub-3 nm particles, the particles critical for understanding NPF. Here we present the Condensation Particle Counters For Atmospheric Rapid Measurements (CPC FARM), a method to measure the concentrations of freshly nucleated particles. The CPC FARM consists of five CPCs operating in parallel, each configured to operate at different detectable particle sizes between 1–3 nm. This study explores two methods to calculate the size distribution from the differential measurements across the CPC channels. The performance of both inversion methods was tested against the size distribution measured by a pair of stepping particle mobility sizers (SMPSs) during an ambient air sampling study in Pittsburgh, PA. Observational results indicate that the CPC FARM is more accurate with higher time resolution and sensitivity in the sub-3 nm range compared to the SMPS.
Cheng, Darren [Carnegie Mellon Univ., Pittsburgh, ↗
R “SHINY” GUI DEVELOPMENT FOR URANIUM ISOTOPIC ANALYSIS WITH MATRIX-ASSISTED IONIZATION MASS SPECTROMETRY
The international nuclear safeguards community continues to seek rapid, accurate, and precise characterization capabilities for the in-field measurement of uranium isotopic compositions in nuclear facilities. Mass spectrometry (MS) is considered the “gold standard” for analysis of relatively long-lived actinides such as uranium (U) and plutonium; however, conventional MS analysis often requires time consuming sample preparation and complex analytical methodologies that are difficult to perform in-field or in-facility. Matrix assisted ionization (MAI) is a novel ambient ionization MS technique (i.e., MAI-MS) that potentially addresses these challenges due to the relative simplicity of the ionization phenomenon and ruggedness of ambient MS instrumentation. Savannah River National Laboratory (SRNL, USA) has demonstrated this technique for nanogram-level 235U/238U isotope ratio measurements within seconds, with percent-level analytical uncertainties capable of discriminating depleted, natural, and low-enriched uranium. Current experimental work on developing MAI methods for uranium isotopic analysis has been enabled by parallel development of a comprehensive MAI-MS data analysis suite at SRNL. Development of this bespoke data analysis software was necessary because commercially available ambient MS software is poorly suited for uranium isotope ratio measurement. The effort leverages the power of R, a popular open-source programming language, and Shiny, an R package providing tools for graphical user interface (GUI) and web interface coding. This software allows researchers without any programming experience to harness and utilize R’s considerable data analysis/visualization power.
LaBone, Elizabeth D.↗
Coupling CTF to MPACT for Improved Thermal-Hydraulic Feedback for Transients
As computational power and techniques continue to advance, reactor analysis codes are afforded the opportunity to employ a more detailed physics model. One area where this has manifested is with coupled neutron kinetics and thermal-hydraulics codes for transient analysis, in which the feedback is critical for accurate modeling. The Michigan Parallel Characteristics Transport (MPACT) code is a 3-D method of characteristics neutron transport code capable of generating sub-pin level power distributions being developed by the University of Michigan through the Consortium for Advanced Simulation of LWRs (CASL) program. Currently, MPACT handles thermal-hydraulic feedback with an internal 1-D radial heat transfer model assuming constant moderator temperature. While this relatively simple treatment of thermal-hydraulic feedback has been shown to accurately model transients where Doppler feedback is the dominant feedback mechanism, coupling MPACT to a detailed thermal-hydraulic code will greatly expand the range of transient problems that can be accurately modeled. COBRA-TF (CTF) is a 3-D two-phase flow, subchannel thermal-hydraulics code maintained by Penn State University through CASL. CTF is based upon the Semi-Implicit Method for Pressure-Linked Equations, and it is especially well suited to model heat transfer and fluid flow phenomena associated with a nuclear reactor through a wide range of conditions. We present an initial effort coupling MPACT to CTF for transients, which provides a wider range of transient problems that can be modeled with increased accuracy. We have successfully coupled the thermal-hydraulics code CTF to the neutronics code MPACT for transient calculations by implicit and Crank-Nicolson methods, which have been demonstrated with single pin and 3x3 configurations. This capability extends the ability of MPACT to accurately model transients through a wider range of conditions than the existing thermal-hydraulic feedback, which is severely limited by the assumption of constant moderator temperature and density. By employing CTF for the thermal- hydraulic feedback, the transient physics can be described more completely at minimal computational expense. (authors)
42 ENGINEERING↗
Efficient quadrature rules for finite element discretizations of nonlocal equations
Here, in this paper, we design efficient quadrature rules for finite element (FE) discretizations of nonlocal diffusion problems with compactly supported kernel functions. Two of the main challenges in nonlocal modeling and simulations are the prohibitive computational cost and the nontrivial implementation of discretization schemes, especially in three-dimensional settings. In this work, we circumvent both challenges by introducing a parametrized mollifying function that improves the regularity of the integrand, utilizing an adaptive integration technique, and exploiting parallelization. We first show that the “mollified” solution converges to the exact one as the mollifying parameter vanishes, then we illustrate the consistency and accuracy of the proposed method on several two- and three-dimensional test cases. Furthermore, we demonstrate the good scaling properties of the parallel implementation of the adaptive algorithm and we compare the proposed method with recently developed techniques for efficient FE assembly.
97 MATHEMATICS AND COMPUTING↗
SU-E-T-499: Initial Developments of An OpenCL-Based Cross-Platform Monte Carlo Dose Engine for Carbon Ion Therapy
Purpose Dose calculation is of critical importance for carbon ion therapy. Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and of all the more fundamental physical quantities related to biological effects. The long computation time, however, limits its routine clinical applications. We have recently started developing a fast MC package, gCMC for carbon therapy on a parallel processing platform, e.g. GPU, aiming at achieving sufficient efficiency to enable MC in clinically important tasks. This abstract reports our progress. Methods gCMC was developed in OpenCL environment. Our initial developments focused on water material. gCMC supported carbon ion transport in the energy range of 1–450 MeV/u. A Class II condensed history algorithm was implemented for charged particle transport simulations with stopping power computed via Bethe-Bloch equation. Energy straggling and multiple scattering were modeled. Total cross section of nuclear interaction was extracted from Geant4. At present, nuclear interaction events were sampled but transports of secondary particles were not included. Results We tested cases with a homogeneous water phantom and a pencil carbon ion beam with energy of 200–400 MeV/u. When only electro-magnetic channel was included, dose/fluence difference between gCMC and Geant4 results averaged within 10% isodose line was <0.5% of the maximum dose/fluence. After enabling nuclear interactions without transporting secondary particles, dose and fluence agreed with the corresponding results computed by Geant4 with <1% difference. Due to the support for multiple platforms of OpenCL, gCMC was executable on NVidia and AMD GPUs, and Intel CPUs. It took ∼50 sec to transport 107 200MeV/u source carbon ions on an NVidia Titan GPU card. Conclusion Preliminary studies have demonstrated the accuracy and efficiency of gCMC. With further developments in near future, gCMC will potentially achieve clinically acceptable fast and accurate MC simulations for carbon ion therapy.
60 APPLIED LIFE SCIENCES↗
Towards Feature-Preserving 2D and 3D Vector Field Compression
The objective of this work is to develop error-bounded lossy compression methods to preserve topological features in 2D and 3D vector fields. Specifically, we explore the preservation of critical points in piecewise linear vector fields. We define the preservation of critical points as, without any false positive, false negative, or false type change in the decompressed data, (1) keeping each critical point in its original cell and (2) retaining the type of each critical point (e.g., saddle and attracting node). The key to our method is to adapt a vertex-wise error bound for each grid point and to compress input data together with the error bound field using a modified lossy compressor. Our compression algorithm can be also embarrassingly parallelized for large data handling and in situ processing. We benchmark our method by comparing it with existing lossy compressors in terms of false positive/negative/type rates, compression ratio, and various vector field visualizations with several scientific applications.
critical points↗
Three paths toward the quantum angle operator
We examine mathematical questions around angle (or phase) operator associated with a number operator through a short list of basic requirements. We implement three methods of construction of quantum angle. The first one is based on operator theory and parallels the definition of angle for the upper half-circle through its cosine and completed by a sign inversion. The two other methods are integral quantization generalizing in a certain sense the Berezin–Klauder approaches. One method pertains to Weyl–Heisenberg integral quantization of the plane viewed as the phase space of the motion on the line. It depends on a family of “weight” functions on the plane. The third method rests upon coherent state quantization of the cylinder viewed as the phase space of the motion on the circle. The construction of these coherent states depends on a family of probability distributions on the line.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
SU-E-T-75: A Simple Technique for Proton Beam Range Verification
Purpose: To develop a measurement-based technique to verify the range of proton beams for quality assurance (QA). Methods: We developed a simple technique to verify the proton beam range with in-house fabricated devices. Two separate devices were fabricated; a clear acrylic rectangular cuboid and a solid polyvinyl chloride (PVC) step wedge. For efficiency in our clinic, we used the rectangular cuboid for double scattering (DS) beams and the step wedge for pencil beam scanning (PBS) beams. These devices were added to our QA phantom to measure dose points along the distal fall-off region (between 80% and 20%) in addition to dose at mid-SOBP (spread out Bragg peak) using a two-dimensional parallel plate chamber array (MatriXX™, IBA Dosimetry, Schwarzenbruck, Germany). This method relies on the fact that the slope of the distal fall-off is linear and does not vary with small changes in energy. Using a multi-layer ionization chamber (Zebra™, IBA Dosimetry), percent depth dose (PDD) curves were measured for our standard daily QA beams. The range (energy) for each beam was then varied (i.e. ±2mm and ±5mm) and additional PDD curves were measured. The distal fall-off of all PDD curves was fit to a linear equation. The distal fall-off measured dose for a particular beam was used in our linear equation to determine the beam range. Results: The linear fit of the fall-off region for the PDD curves, when varying the range by a few millimeters for a specific QA beam, yielded identical slopes. The calculated range based on measured point dose(s) in the fall-off region using the slope resulted in agreement of ±1mm of the expected beam range. Conclusion: We developed a simple technique for accurately verifying the beam range for proton therapy QA programs.
60 APPLIED LIFE SCIENCES↗
An experimental comparison of a space-time multigrid method with PFASST for a reaction-diffusion problem
We consider two parallel-in-time approaches applied to a (reaction) diffusion problem, possibly non-linear. In particular, we consider PFASST (Parallel Full Approximation Scheme in Space and Time) and space-time multigrid strategies. For both approaches, we start from an integral formulation of the continuous time dependent problem. Then, a collocation form for PFASST and a discontinuous Galerkin discretization in time for the space-time multi-grid are employed, resulting in the same discrete solution at the time nodes. Strong and weak scaling of both multilevel strategies are compared for varying orders of the temporal discretization. Moreover, we investigate the respective convergence behavior for non-linear problems and highlight quantitative differences in execution times
97 MATHEMATICS AND COMPUTING↗
Massively-parallel electron dynamics calculations in real-time and real-space: Toward applications to nanostructures of more than ten-nanometers in size
A highly efficient program of massively parallel calculations for electron dynamics has been developed in an effort to apply the method to optical response of nanostructures of more than ten-nanometers in size. The approach is based on time-dependent density functional theory calculations in real-time and real-space. The computational code is implemented by using simple algorithms with a finite-difference method in space derivative and Taylor expansion in time-propagation. Since the computational program is free from the algorithms of eigenvalue problems and fast-Fourier-transformation, which are usually implemented in conventional quantum chemistry or band structure calculations, it is highly suitable for massively parallel calculations. Benchmark calculations using the K computer at RIKEN demonstrate that the parallel efficiency of the program is very high on more than 60 000 CPU cores. The method is applied to optical response of arrays of C{sub 60} orderly nanostructures of more than 10 nm in size. The computed absorption spectrum is in good agreement with the experimental observation.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
The divide-expand-consolidate coupled cluster scheme: Divide-expand-consolidate coupled cluster
The Divide-Expand-Consolidate (DEC) scheme is a linear-scaling and massively parallel framework for high accuracy coupled cluster (CC) calculations on large molecular systems. It is designed as a black-box method, which ensures error control in the correlation energy and molecular properties. DEC is combined with a massively parallel implementation to fully utilize modern many core architectures providing a fast time to solution. The implementation ensures performance portability and will straightforwardly benefit from new hardware developments. The DEC scheme has been applied to several levels of CC theory and extended the range of application of those methods.
Chemistry↗
Performance Analysis and Optimal Node-aware Communication for Enlarged Conjugate Gradient Methods
Krylov methods are a key way of solving large sparse linear systems of equations but suffer from poor strong scalability on distributed memory machines. Furthermore, this is due to high synchronization costs from large numbers of collective communication calls alongside a low computational workload. Enlarged Krylov methods address this issue by decreasing the total iterations to convergence, an artifact of splitting the initial residual and resulting in operations on block vectors. In this article, we present a performance study of an enlarged Krylov method, Enlarged Conjugate Gradients (ECG), noting the impact of block vectors on parallel performance at scale. Most notably, we observe the increased overhead of point-to-point communication as a result of denser messages in the sparse matrix-block vector multiplication kernel. Additionally, we present models to analyze expected performance of ECG, as well as motivate design decisions. Most importantly, we introduce a new point-to-point communication approach based on node-aware communication techniques that increases efficiency of the method at scale.
97 MATHEMATICS AND COMPUTING↗
HIGH-FIDELITY SIMULATION-DRIVEN MODEL DEVELOPMENT FOR COARSE-GRAINED COMPUTATIONAL FLUID DYNAMICS
Nuclear reactor safety analysis requires identifying various credible accident scenarios and determining their consequences. For a full-scale nuclear power plant system behavior, it is impossible to obtain sufficient experimental data for a broad range of risk-significant accident scenarios. In single-phase flow convective problems, Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) can provide us with high fidelity results when physical data are unavailable. However, these methods are computationally expensive and cannot be afforded for simulation of long transient scenarios in nuclear accidents despite extraordinary advances in high performance scientific computing over the past decades. The major issue is the inability to make the transient computation parallel, thus making number of time steps required in high-fidelity methods unaffordable for long transients. In this work, we propose to apply a high fidelity simulation-driven approach to model sub-grid scale (SGS) effect in Coarse Grained Computational Fluid Dynamics CG-CFD. This approach aims to develop a statistical surrogate model instead of the deterministic SGS model. We chose to start with a turbulent natural convection case with volumetric heating in a horizontal fluid layer with a rigid, insulated lower boundary and isothermal (cold) upper boundary. This scenario of unstable stratification is relevant to turbulent natural convection in a molten corium pool during a severe nuclear reactor accident, as well as in containment mixing and passive cooling. The presented approach demonstrates how to create a correction for the CG-CFD solution by modifying the energy balance equation. A global correction for the temperature equation proves to achieve a significant improvement to the prediction of steady state temperature distribution through the fluid layer.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Analytic energy gradient of excited electronic state within TDDFT/MMpol framework: Benchmark tests and parallel implementation
The time-dependent density functional theory (TDDFT) has become the most popular method to calculate the electronic excitation energies, describe the excited-state properties, and perform the excited-state geometric optimization of medium and large-size molecules due to the implementation of analytic excited-state energy gradient and Hessian in many electronic structure software packages. To describe the molecules in condensed phase, one usually adopts the computationally efficient hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) models. Here, we extend our previous work on the energy gradient of TDDFT/MM excited state to account for the mutual polarization effects between QM and MM regions, which is believed to hold a crucial position in the potential energy surface of molecular systems when the photoexcitation-induced charge rearrangement in the QM region is drastic. The implementation of a simple polarizable TDDFT/MM (TDDFT/MMpol) model in Q-Chem/CHARMM interface with both the linear response and the state-specific features has been realized. Several benchmark tests and preliminary applications are exhibited to confirm our implementation and assess the effects of different treatment of environmental polarization on the excited-state properties, and the efficiency of parallel implementation is demonstrated as well.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗