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At least 1,225 records · Page 68

All sources NASA NTRS DOE OSTI

DOE OSTI2016

FARGO3D: A NEW GPU-ORIENTED MHD CODE

We present the FARGO3D code, recently publicly released. It is a magnetohydrodynamics code developed with special emphasis on the physics of protoplanetary disks and planet–disk interactions, and parallelized with MPI. The hydrodynamics algorithms are based on finite-difference upwind, dimensionally split methods. The magnetohydrodynamics algorithms consist of the constrained transport method to preserve the divergence-free property of the magnetic field to machine accuracy, coupled to a method of characteristics for the evaluation of electromotive forces and Lorentz forces. Orbital advection is implemented, and an N-body solver is included to simulate planets or stars interacting with the gas. We present our implementation in detail and present a number of widely known tests for comparison purposes. One strength of FARGO3D is that it can run on either graphical processing units (GPUs) or central processing units (CPUs), achieving large speed-up with respect to CPU cores. We describe our implementation choices, which allow a user with no prior knowledge of GPU programming to develop new routines for CPUs, and have them translated automatically for GPUs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Localized Exponential Time Differencing Method for Shallow Water Equations: Algorithms and Numerical Study

Here, we explore the performance of the exponential time differencing (ETD) method applied to the rotating shallow water equations. Comparing with explicit time stepping of the same order accuracy in time, the ETD algorithms could reduce the computational time in many cases by allowing the use of large time step sizes while still maintaining numerical stability. To accelerate the ETD simulations, we propose a localized approach that synthesizes the ETD method and overlapping domain decomposition. By dividing the original problem into many subdomain problems of smaller sizes and solving them locally, the proposed approach could speed up the calculation of matrix exponential vector products. Several standard test cases for shallow water equations of one or multiple layers are considered. The results show great potential of the localized ETD method for high-performance computing because each subdomain problem can be naturally solved in parallel at every time step.

58 GEOSCIENCES↗

DOE OSTI2013

Peptide mediators of cholesterol efflux

The present invention provides a family of non-naturally occurring polypeptides having cholesterol efflux activity that parallels that of full-length apolipoproteins (e.g., Apo AI and Apo E), and having high selectivity for ABAC1 that parallels that of full-length apolipoproteins. The invention also provides compositions comprising such polypeptides, methods of identifying, screening and synthesizing such polypeptides, and methods of treating, preventing or diagnosing diseases and disorders associated with dyslipidemia, hypercholesterolemia and inflammation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Potent and selective mediators of cholesterol efflux

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Thermo mechanical analysis of fully ceramic microencapsulated fuel during in-pile operation

A proposed fuel for improved performance in LWRs (Light Water Reactors) is FCM (fully encapsulated micro-ceramic) fuel concept that involves TRISO (Tri-structural-Isotropic) fuel particles embedded in a NITE (Nano Infiltrated Eutectic) silicon carbide matrix. TRISO fuel particles contain a spherical fuel kernel that will likely range from about 500 to in excess of 800 μm in diameter. The kernel and buffer layer are then typically coated with 3 isotropic layers consisting of a dense inner pyrolytic carbon (IPyC), a silicon carbide (SiC) layer, and an outer layer of dense, pyrolytic carbon (OPyC). These layers are typically around 40 μm thick, but can range from 20 to 60 μm. The TRISO particle packing fraction in the NITE-SiC matrix is expected to be 40-45 vol.%. The release of radioactivity into the coolant is dependent on the integrity of the silicon carbide layer of the TRISO particles and the NITE-SiC matrix. BISON, a code under development by Idaho National Laboratory, has been built on the Multi-physics Object Oriented Simulation Environment (MOOSE). MOOSE is a massively parallel, finite element computational system that uses a Jacobian-free, Newton-Krylov (JFNK) method to solve coupled systems and non-linear partial differential equations. A single particle comparison to fuel performance codes such as PARFUME was conducted and demonstrated that BISON is able to simulate the required physics. FCM pellets embedded with homogenous particles were simulated. It was found that the interior matrix temperature was predicted to be considerably lower than for an equivalent UO{sub 2} pellet. The swelling dependence on temperature created a compressive region around the perimeter of the pellet. However, at fluences above 6.10{sup 25} neutrons/m{sup 2}, the swelling of the pyrolytic carbon might cause significant tensile stresses and possible cracks near the surface of the pellet. This suggests that the pyrolytic carbon swelling may be an important factor in the lifetime of this fuel type.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Views on Long-Term Safety of Deep Borehole Disposal - 16657

The Swedish Nuclear Fuel and Waste Management Co., SKB, has since the end of the 1980s evaluated Deep Borehole Disposal (DBD), of spent nuclear fuel (SNF). This has been done in parallel with the development of a mined repository concept based on the KBS-3V method. The most recent evaluation involved a broad comparison between the KBS-3V method and DBD. The comparison highlights differences between the two methods in the whole chain of the SNF handling including premises for siting, licensing, repository construction, safety during the operational phase, post-closure safety, physical protection, nuclear safeguards, retrieval of the deposited SNF, time planning, need for development, costs and nontechnical project risks. The ambition has been to make an as objective comparison between the two methods as possible, bearing in mind that there are big differences between the two concepts in terms of technical maturity as well as in terms of both quantity and quality of available data. While the primary safety function of the KBS-3V method is long-term containment in a corrosion resistant copper canister, the safety of DBD relies on stagnant groundwater at depth. It is argued in the aforementioned study that this groundwater stagnancy may be jeopardised because of heat and gas evolution in the disposal boreholes, and that deformation of the boreholes make efficient sealing of the deposition boreholes difficult. SKB has taken the position that the DBD method is associated with too many question marks to make it interesting as an alternative method in the Swedish programme. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Optimizing Excited-State Electronic-Structure Codes for Intel Knights Landing: A Case Study on the BerkeleyGW Software

We profile and optimize calculations performed with the BerkeleyGW code on the Xeon-Phi architecture. BerkeleyGW depends both on hand-tuned critical kernels as well as on BLAS and FFT libraries. We describe the optimization process and performance improvements achieved. We discuss a layered parallelization strategy to take advantage of vector, thread and node-level parallelism. We discuss locality changes (including the consequence of the lack of L3 cache) and effective use of the on-package high-bandwidth memory. We show preliminary results on Knights-Landing including a roofline study of code performance before and after a number of optimizations. We find that the GW method is particularly well-suited for many-core architectures due to the ability to exploit a large amount of parallelism over plane-wave components, band-pairs, and frequencies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗

DOE OSTI2013

Steady-State Gyrokinetics Transport Code (SSGKT), A Scientific Application Partnership with the Framework Application for Core-Edge Transport Simulations, Final Report

This project initiated the development of TGYRO - a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale GYRO turbulence simulations into a framework for practical multi-scale simulation of conventional tokamaks as well as future reactors. Using a lightweight master transport code, multiple independent (each massively parallel) gyrokinetic simulations are coordinated. The capability to evolve profiles using the TGLF model was also added to TGYRO and represents a more typical use-case for TGYRO. The goal of the project was to develop a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale gyrokinetic turbulence simulations into a framework for practical multi-scale simulation of a burning plasma core ? the International Thermonuclear Experimental Reactor (ITER) in particular. This multi-scale simulation capability will be used to predict the performance (the fusion energy gain, Q) given the H-mode pedestal temperature and density. At present, projections of this type rely on transport models like GLF23, which are based on rather approximate fits to the results of linear and nonlinear simulations. Our goal is to make these performance projections with precise nonlinear gyrokinetic simulations. The method of approach is to use a lightweight master transport code to coordinate multiple independent (each massively parallel) gyrokinetic simulations using the GYRO code. This project targets the practical multi-scale simulation of a reactor core plasma in order to predict the core temperature and density profiles given the H-mode pedestal temperature and density. A master transport code will provide feedback to O(16) independent gyrokinetic simulations (each massively parallel). A successful feedback scheme offers a novel approach to predictive modeling of an important national and international problem. Success in this area of fusion simulations will allow US scientists to direct the research path of ITER over the next two decades. The design of an efficient feedback algorithm is a serious numerical challenge. Although the power source and transport balance coding in the master are standard, it is nontrivial to design a feedback loop that can cope with outputs that are both intermittent and extremely expensive. A prototypical feedback scheme has already been successfully demonstrated for a single global GYRO simulation, although the robustness and efficiency are likely far from optimal. Once the transport feedback scheme is perfected, it could, in principle, be embedded into any of the more elaborate transport codes (ONETWO, TRANSP, and CORSICA), or adopted by other FSP-related multi-scale projects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

A Method to Alleviate the Long History Problem Encountered in Monte Carlo Simulations via Weight Window Variance Reduction

When the weight window is implemented in large and complex models, streaming path and deep penetration could lead to a long history problem that takes a disproportionate amount of time for the accomplishment of Monte Carlo simulations and exerts a detrimental effect on the efficiency of parallel computing. An approach set the limitation of weight window splitting was proposed for the alleviation of long history problem. Tests were conducted on a streaming dog-leg geometry model and a 3D model of the Chinese Fusion Engineering Testing Reactor. The results show that a suitable parameter in the alleviation method could optimize both the performance of variance reduction and the efficiency of parallel calculation, which makes long history problem tractable.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2013

Dynamic load balancing for petascale quantum Monte Carlo applications: The Alias method

Diffusion Monte Carlo is the most accurate widely used Quantum Monte Carlo method for the electronic structure of materials, but it requires frequent load balancing or population redistribution steps to maintain efficiency and avoid accumulation of systematic errors on parallel machines. The load balancing step can be a significant factor affecting performance, and will become more important as the number of processing elements increases. We propose a new dynamic load balancing algorithm, the Alias Method, and evaluate it theoretically and empirically. An important feature of the new algorithm is that the load can be perfectly balanced with each process receiving at most one message. It is also optimal in the maximum size of messages received by any process. We also optimize its implementation to reduce network contention, a process facilitated by the low messaging requirement of the algorithm. Empirical results on the petaflop Cray XT Jaguar supercomputer at ORNL showing up to 30% improvement in performance on 120,000 cores. The load balancing algorithm may be straightforwardly implemented in existing codes. The algorithm may also be employed by any method with many near identical computational tasks that requires load balancing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

High Order Wall-Modeled Large-Eddy Simulation on Mixed Unstructured Meshes

In the present study, an algebraic equilibrium wall model previously developed for hexahedral elements is extended to handle mixed meshes including prismatic, tetrahedral, and pyramidal elements in the context of a discontinuous high-order method. This extension is needed for complex geometries, for which high-order mixed elements (e.g., tetrahedral and pyramidal elements) are often necessary near solid walls to avoid meshing challenges. Various design decisions are discussed to achieve the best performance on massively parallel CPU/GPU architectures for a production-level high-order large-eddy simulation solver based on the flux reconstruction/correction procedure via reconstruction method, hpMusic. The extension to other elements is first evaluated using a benchmark channel flow problem at various Reynolds numbers. After that, flow over the NASA high-lift Common Research Model (CRM-HL) from the 4th AIAA High-lift Prediction Workshop is computed to further test the new implementation. Computational results at the third- and fourth-order accuracies are compared with experimental data.

Engineering↗

DOE OSTI2025

Safe Reinforcement Learning-Based Transient Stability Control for Islanded Microgrids With Topology Reconfiguration

This paper proposes a safe reinforcement learning (RL)-based transient stability emergency control (TSEC) method for islanded microgrids. RL requires extensive interaction with the environment to learn control strategies, hence, a data-driven approach is used as a substitute for time-consuming time-domain simulation calculations. Deep sigma point processes (DSPP), which is a Gaussian process model, is utilized to predict the normal distribution of transient stability of microgrids and to construct a transient stability chance constraint. Reward-constrained policy optimization (RCPO) can simultaneously achieve objective prediction, policy learning, and constraint cost coefficient update across multiple timescales. RCPO interacts with the DSPP-based microgrid environment through a multi-process parallel manner, greatly increasing the training speed. Case studies on a real islanded microgrid demonstrate that the proposed method can efficiently and quickly obtain the optimal emergency control strategy while adhering to all hard constraints.

14 SOLAR ENERGY↗

DOE OSTI2014

Stochastic, real-space, imaginary-time evaluation of third-order Feynman–Goldstone diagrams

A new, alternative set of interpretation rules of Feynman–Goldstone diagrams for many-body perturbation theory is proposed, which translates diagrams into algebraic expressions suitable for direct Monte Carlo integrations. A vertex of a diagram is associated with a Coulomb interaction (rather than a two-electron integral) and an edge with the trace of a Green's function in real space and imaginary time. With these, 12 diagrams of third-order many-body perturbation (MP3) theory are converted into 20-dimensional integrals, which are then evaluated by a Monte Carlo method. It uses redundant walkers for convergence acceleration and a weight function for importance sampling in conjunction with the Metropolis algorithm. The resulting Monte Carlo MP3 method has low-rank polynomial size dependence of the operation cost, a negligible memory cost, and a naturally parallel computational kernel, while reproducing the correct correlation energies of small molecules within a few mE{sub h} after 10{sup 6} Monte Carlo steps.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Preliminary performance evaluation of P++ single event proton scattering algorithms on GPUS - 25688

A need has been realized for fast, accurate charged particle transport in a wide variety of domains. Utilizing hardware acceleration through GPUs now common in user desktops, speedups in simulation comparable to those found with HPC systems can be realized for a fraction of the price. Preliminary results on the P++ proton transport code developed by the Rensselaer Radiation Measurement and Dosimetry Group (RRMDG) are presented. The code has been validated for the 1 GeV to 1 MeV energy regime and is targeted to benefit application areas such as proton radiography, space radiation research, and clinical accelerator therapy. The code is notable for employing a single event, 'on the fly' cross section based transport algorithm rather than the traditional condensed history or step based method seen in many production Monte Carlo codes. Performance improvements for the P++ code have been introduced through MPI parallelization as well as a CUDA version of the transport algorithm capable of running on NVidia GPUs. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2016

Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, used for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Development of ARCHER towards clinical use: modeling and simulation of Varian Linac for radiation therapy dose calculations - 25449

Monte Carlo particle transport methods are well recognized as the most accurate approach to dose calculations for radiation therapy treatment planning. However, the lengthy calculation time has prevented Monte Carlo methods from being applied to dose calculations in the planning of radiation therapy. Recently, the emerging parallel computing hardware accelerators, such as general-purpose Graphics Processing Unit (GPU), have significantly boosted the performance of Monte Carlo codes. The accuracy of a clinical dose engine depends greatly on the accuracy of source term modeling and the methodology of dose calculations. Hence, in this study, an efficient and accurate source model of the Varian TrueBeam{sup R} Linac is developed and integrated with a fast photon-electron transport module of the recently developed high-performance Monte Carlo code, ARCHER. The validity of the source model and the particle transport physics are verified with established dose calculation codes such as EGSnrc and validated with experimental measurements. To demonstrate the capability of the platform in clinical applications, three clinical treatment plans (the lung, breast, and prostate) are simulated and analyzed. From the perspective of performance, the entire simulation of each clinical plan, starting from the source modeling to the end of particle transport within the patient phantom, can be finished in less than one minute using a single Titan X GPU card with 1% statistical error. In comparison, the same cases take the EGSnrc code hundreds of CPU hours to finish. The results suggest that this new version of ARCHER code has been successfully developed and tested as a clinically deployable dose engine for external photon beam IMRT plans in the clinical setting. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2016

Monte Carlo Techniques for Nuclear Systems - Theory Lectures

These are lecture notes for a Monte Carlo class given at the University of New Mexico. The following topics are covered: course information; nuclear eng. review & MC; random numbers and sampling; computational geometry; collision physics; tallies and statistics; eigenvalue calculations I; eigenvalue calculations II; eigenvalue calculations III; variance reduction; parallel Monte Carlo; parameter studies; fission matrix and higher eigenmodes; doppler broadening; Monte Carlo depletion; HTGR modeling; coupled MC and T/H calculations; fission energy deposition. Solving particle transport problems with the Monte Carlo method is simple - just simulate the particle behavior. The devil is in the details, however. These lectures provide a balanced approach to the theory and practice of Monte Carlo simulation codes. The first lectures provide an overview of Monte Carlo simulation methods, covering the transport equation, random sampling, computational geometry, collision physics, and statistics. The next lectures focus on the state-of-the-art in Monte Carlo criticality simulations, covering the theory of eigenvalue calculations, convergence analysis, dominance ratio calculations, bias in Keff and tallies, bias in uncertainties, a case study of a realistic calculation, and Wielandt acceleration techniques. The remaining lectures cover advanced topics, including HTGR modeling and stochastic geometry, temperature dependence, fission energy deposition, depletion calculations, parallel calculations, and parameter studies. This portion of the class focuses on using MCNP to perform criticality calculations for reactor physics and criticality safety applications. It is an intermediate level class, intended for those with at least some familiarity with MCNP. Class examples provide hands-on experience at running the code, plotting both geometry and results, and understanding the code output. The class includes lectures & hands-on computer use for a variety of Monte Carlo calculations. Beginning MCNP users are encouraged to review LA-UR-09-00380, "Criticality Calculations with MCNP: A Primer (3nd Edition)" (available at http:// mcnp.lanl.gov under "Reference Collection") prior to the class. No Monte Carlo class can be complete without having students write their own simple Monte Carlo routines for basic random sampling, use of the random number generator, and simplified particle transport simulation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗