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At least 451 records · Page 25

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DOE OSTI2015

Forces and stress in second order Møller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach

The forces acting on the atoms as well as the stress tensor are crucial ingredients for calculating the structural and dynamical properties of systems in the condensed phase. Here, these derivatives of the total energy are evaluated for the second-order Møller-Plesset perturbation energy (MP2) in the framework of the resolution of identity Gaussian and plane waves method, in a way that is fully consistent with how the total energy is computed. This consistency is non-trivial, given the different ways employed to compute Coulomb, exchange, and canonical four center integrals, and allows, for example, for energy conserving dynamics in various ensembles. Based on this formalism, a massively parallel algorithm has been developed for finite and extended system. The designed parallel algorithm displays, with respect to the system size, cubic, quartic, and quintic requirements, respectively, for the memory, communication, and computation. All these requirements are reduced with an increasing number of processes, and the measured performance shows excellent parallel scalability and efficiency up to thousands of nodes. Additionally, the computationally more demanding quintic scaling steps can be accelerated by employing graphics processing units (GPU’s) showing, for large systems, a gain of almost a factor two compared to the standard central processing unit-only case. In this way, the evaluation of the derivatives of the RI-MP2 energy can be performed within a few minutes for systems containing hundreds of atoms and thousands of basis functions. With good time to solution, the implementation thus opens the possibility to perform molecular dynamics (MD) simulations in various ensembles (microcanonical ensemble and isobaric-isothermal ensemble) at the MP2 level of theory. Geometry optimization, full cell relaxation, and energy conserving MD simulations have been performed for a variety of molecular crystals including NH{sub 3}, CO{sub 2}, formic acid, and benzene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2013

DIRECT INTEGRATION OF THE COLLISIONLESS BOLTZMANN EQUATION IN SIX-DIMENSIONAL PHASE SPACE: SELF-GRAVITATING SYSTEMS

We present a scheme for numerical simulations of collisionless self-gravitating systems which directly integrates the Vlasov-Poisson equations in six-dimensional phase space. Using the results from a suite of large-scale numerical simulations, we demonstrate that the present scheme can simulate collisionless self-gravitating systems properly. The integration scheme is based on the positive flux conservation method recently developed in plasma physics. We test the accuracy of our code by performing several test calculations, including the stability of King spheres, the gravitational instability, and the Landau damping. We show that the mass and the energy are accurately conserved for all the test cases we study. The results are in good agreement with linear theory predictions and/or analytic solutions. The distribution function keeps the property of positivity and remains non-oscillatory. The largest simulations are run on 64{sup 6} grids. The computation speed scales well with the number of processors, and thus our code performs efficiently on massively parallel supercomputers.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

redMaPPer. I. Algorithm and SDSS DR8 catalog

We describe redMaPPer, a new red sequence cluster finder specifically designed to make optimal use of ongoing and near-future large photometric surveys. The algorithm has multiple attractive features: (1) it can iteratively self-train the red sequence model based on a minimal spectroscopic training sample, an important feature for high-redshift surveys. (2) It can handle complex masks with varying depth. (3) It produces cluster-appropriate random points to enable large-scale structure studies. (4) All clusters are assigned a full redshift probability distribution P(z). (5) Similarly, clusters can have multiple candidate central galaxies, each with corresponding centering probabilities. (6) The algorithm is parallel and numerically efficient: it can run a Dark Energy Survey-like catalog in ∼500 CPU hours. (7) The algorithm exhibits excellent photometric redshift performance, the richness estimates are tightly correlated with external mass proxies, and the completeness and purity of the corresponding catalogs are superb. We apply the redMaPPer algorithm to ∼10, 000 deg{sup 2} of SDSS DR8 data and present the resulting catalog of ∼25,000 clusters over the redshift range z in [0.08, 0.55]. The redMaPPer photometric redshifts are nearly Gaussian, with a scatter σ {sub z} ≈ 0.006 at z ≈ 0.1, increasing to σ {sub z} ≈ 0.02 at z ≈ 0.5 due to increased photometric noise near the survey limit. The median value for |Δz|/(1 + z) for the full sample is 0.006. The incidence of projection effects is low (≤5%). Detailed performance comparisons of the redMaPPer DR8 cluster catalog to X-ray and Sunyaev-Zel'dovich catalogs are presented in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2010

FAST AND OPTIMAL COSMIC MICROWAVE BACKGROUND LENSING USING STATISTICAL INTERPOLATION ON THE SPHERE

We describe an accurate and fast pixel-based statistical method to interpolate fields of arbitrary spin on the sphere. We call this method Fast and Lean Interpolation on the Sphere (FLINTS). The method predicts the optimal interpolated values based on the theory of isotropic Gaussian random fields and provides an accurate error estimate at no additional cost. We use this method to compute lensed cosmic microwave background (CMB) maps precisely and quickly, achieving a relative precision of 0.02% at a HEALPIX resolution of N {sub side} = 4096, for a bandlimit of l{sub max}= 4096 in the same time it takes to simulate the original, unlensed CMB map. The method is suitable for efficient, distributed memory parallelization. The power spectra of our lensed maps are accurate to better than 0.5% at l= 3000 for the temperature, the E and B modes of the polarization. As expected theoretically, we demonstrate that, on realistic cases, this method is between two and three orders of magnitude more precise than other known interpolation methods for the same computational cost.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Explicit structure-preserving geometric particle-in-cell algorithm in curvilinear orthogonal coordinate systems and its applications to whole-device 6D kinetic simulations of tokamak physics

Explicit structure-preserving geometric particle-in-cell (PIC) algorithm in curvilinear orthogonal coordinate systems is developed. The work reported represents a further development of the structure-preserving geometric PIC algorithm achieving the goal of practical applications in magnetic fusion research. The algorithm is constructed by discretizing the field theory for the system of charged particles and electromagnetic field using Whitney forms, discrete exterior calculus, and explicit non-canonical symplectic integration. In addition to the truncated infinitely dimensional symplectic structure, the algorithm preserves exactly many important physical symmetries and conservation laws, such as local energy conservation, gauge symmetry and the corresponding local charge conservation. As a result, the algorithm possesses the long-term accuracy and fidelity required for first-principles-based simulations of the multiscale tokamak physics. The algorithm has been implemented in the SymPIC code, which is designed for high-efficiency massively-parallel PIC simulations in modern clusters. The code has been applied to carry out whole-device 6D kinetic simulation studies of tokamak physics. A self-consistent kinetic steady state for fusion plasma in the tokamak geometry is numerically found with a predominately diagonal and anisotropic pressure tensor. The state also admits a steady-state sub-sonic ion flow in the range of 10 km s -1 , agreeing with experimental observations and analytical calculations Kinetic ballooning instability in the self-consistent kinetic steady state is simulated. It is shown that high-n ballooning modes have larger growth rates than low-n global modes, and in the nonlinear phase the modes saturate approximately in 5 ion transit times at the 2% level by the E × B flow generated by the instability. These results are consistent with early and recent electromagnetic gyrokinetic simulations.

43 PARTICLE ACCELERATORS↗

DOE OSTI2018

Umbrella sampling: a powerful method to sample tails of distributions

We present the umbrella sampling (US) technique and show that it can be used to sample extremely low-probability areas of the posterior distribution that may be required in statistical analyses of data. In this approach sampling of the target likelihood is split into sampling of multiple biased likelihoods confined within individual umbrella windows. We show that the US algorithm is efficient and highly parallel and that it can be easily used with other existing Markov Chain Monte Carlo (MCMC) samplers. The method allows the user to capitalize on their intuition and define umbrella windows and increase sampling accuracy along specific directions in the parameter space. Alternatively, one can define umbrella windows using an approach similar to parallel tempering. We provide a public code that implements US as a standalone PYTHON package. We present a number of tests illustrating the power of the US method in sampling low-probability areas of the posterior and show that this ability allows a considerably more robust sampling of multimodal distributions compared to standard sampling methods. We also present an application of the method in a real world example of deriving cosmological constraints using the supernova type Ia data. We show that US can sample the posterior accurately down to the approximate to 15 sigma credible region in the Omega(m) - Omega(Lambda) plane, while for the same computational effort the affine-invariant MCMC sampling implemented in the emcee code samples the posterior reliably only to approximate to 3 sigma.

cosmology: cosmological parameters↗

DOE OSTI2018

Modular Spiking Neural Circuits for Mapping Long Short-Term Memory on a Neurosynaptic Processor

Due to the distributed and asynchronous nature of neural computation through low-energy spikes, brain-inspired hardware systems offer high energy efficiency and massive parallelism. One such platform is the IBM TrueNorth neurosynaptic system. Recently, TrueNorth compatible representation learning algorithms have emerged, achieving close to the state-of-the-art performance in various data sets. However, its application in temporal sequence processing models, such as recurrent neural networks (RNNs), is still only at the proof of concept level. There is an inherent difficulty in capturing temporal dynamics of an RNN using spiking neurons, which is only exasperated by the hardware constraints in connectivity and synaptic weight resolution. This paper presents a design flow that overcomes these difficulties and maps a special case of recurrent networks called long short-term memory (LSTM) onto a spike-based platform. The framework utilizes various approximation techniques, such as activation discretization, weight quantization, and scaling and rounding, spiking neural circuits that implement the complex gating mechanisms, and a store-and-release technique to enable neuron synchronization and faithful storage. While the presented techniques can be applied to map LSTM to any spiking neural network (SNN) simulator/emulator, here we choose the TrueNorth chip as the target platform by adhering to its hardware constraints. Three LSTM applications, parity check, extended Reber grammar, and question classification, are evaluated. The tradeoffs among accuracy, performance, and energy tradeoffs achieved on TrueNorth are demonstrated. Finally, this is compared with the performance on an SNN platform without hardware constraints, which represents the upper bound of the achievable accuracy.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Automatic Differentiation of C++ Codes on Emerging Manycore Architectures with Sacado

Automatic differentiation (AD) is a well-known technique for evaluating analytic derivatives of calculations implemented on a computer, with numerous software tools available for incorporating AD technology into complex applications. However, a growing challenge for AD is the efficient differentiation of parallel computations implemented on emerging manycore computing architectures such as multicore CPUs, GPUs, and accelerators as these devices become more pervasive. In this work, we explore forward mode, operator overloading-based differentiation of C++ codes on these architectures using the widely available Sacado AD software package. In particular, we leverage Kokkos, a C++ tool providing APIs for implementing parallel computations that is portable to a wide variety of emerging architectures. Here we describe the challenges that arise when differentiating code for these architectures using Kokkos, and two approaches for overcoming them that ensure optimal memory access patterns as well as expose additional dimensions of fine-grained parallelism in the derivative calculation. We describe the results of several computational experiments that demonstrate the performance of the approach on a few contemporary CPU and GPU architectures. We then conclude with applications of these techniques to the simulation of discretized systems of partial differential equations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

PPO And Friends

PPO and Friends (PPOAF) is a pytorch implementation of proximal policy optimization for single- and multi-agent reinforcement learning (the PPO), along with several optimizations and add-ons (the Friends) to enable efficient MPI-parallelized model training on HPC clusters.

Maguire, AlisterO↗

DOE OSTI2025

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

DOE OSTI2013

Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT)

For the past three years, a large analysis and visualization effort—funded by the Department of Energy’s Office of Biological and Environmental Research (BER), the National Aeronautics and Space Administration (NASA), and the National Oceanic and Atmospheric Administration (NOAA)—has brought together a wide variety of industry-standard scientific computing libraries and applications to create Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) to serve the global climate simulation and observational research communities. To support interactive analysis and visualization, all components connect through a provenance application–programming interface to capture meaningful history and workflow. Components can be loosely coupled into the framework for fast integration or tightly coupled for greater system functionality and communication with other components. The overarching goal of UV-CDAT is to provide a new paradigm for access to and analysis of massive, distributed scientific data collections by leveraging distributed data architectures located throughout the world. The UV-CDAT framework addresses challenges in analysis and visualization and incorporates new opportunities, including parallelism for better efficiency, higher speed, and more accurate scientific inferences. Today, it provides more than 600 users access to more analysis and visualization products than any other single source.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Challenges and Recommended Policies for Simultaneous Global Implementation of Low-GWP Refrigerants and High Efficiency in Room Air Conditioners

Increasing incomes, electrification, and urbanization—as well as a warming world—are driving up the global stock of air conditioners (ACs), particularly in emerging economies with hot climates. AC energy consumption is expected to increase substantially as the global stock of room ACs rises to 1.5 billion in 2030 and 2.5 billion in 2050. Hence, improving AC energy efficiency will be critical to reducing AC energy, cost (consumer lifecycle cost, electricity generation cost, etc.), peak load, and emissions impacts. The 2016 Kigali Amendment to the Montreal Protocol offers an opportunity to improve AC energy efficiency in tandem with the phasedown of high global warming potential (GWP) hydrofluorocarbon (HFC) refrigerants. Based on the most recent information, a literature review, and interviews with manufacturers and industry experts, we find the main barriers to deploying high-efficiency ACs include concerns about market demand and cost, which could be mitigated by appropriately improved design of market-transformation programs such as standards and labeling, incentive, and procurement programs. The main barriers to the low-GWP refrigerant transition include the need for timely revision of safety standards and associated costs for capacity-building activities allowing safe use of low-GWP refrigerants in ACs. Policy action and the market transformation can be accelerated by advancing the refrigerant transition and efficiency improvements in parallel.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2011

Sensitivities and Uncertainties Related to Numerics and Building Features in Urban Modeling

Oak Ridge National Laboratory (ORNL) has been engaged in the development and testing of a computational system that would use a grid of activation foil detectors to provide postdetonation forensic information from a nuclear device detonation. ORNL has developed a high-performance, three-dimensional (3-D) deterministic radiation transport code called Denovo. Denovo solves the multigroup discrete ordinates (SN) equations and can output 3-D data in a platform-independent format that can be efficiently analyzed using parallel, high-performance visualization tools. To evaluate the sensitivities and uncertainties associated with the deterministic computational method numerics, a numerical study on the New York City Times Square model was conducted using Denovo. In particular, the sensitivities and uncertainties associated with various components of the calculational method were systematically investigated, including (a) the Legendre polynomial expansion order of the scattering cross sections, (b) the angular quadrature, (c) multigroup energy binning, (d) spatial mesh sizes, (e) the material compositions of the building models, (f) the composition of the foundations upon which the buildings rest (e.g., ground, concrete, or asphalt), and (g) the amount of detail included in the building models. Although Denovo may calculate the idealized model well, there may be uncertainty in the results because of slight departures of the above-named parameters from those used in the idealized calculations. Fluxes and activities at selected locations from perturbed calculations are compared with corresponding values from the idealized or base case to determine the sensitivities associated with specified parameter changes. Results indicate that uncertainties related to numerics can be controlled by using higher fidelity models, but more work is needed to control the uncertainties related to the model.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2011

Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared memory programming interface to manipulate distributed defense arrays. Using a combination of GA and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Scalability studies will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Global Arrays↗

DOE OSTI2016

Collectively loading programs in a multiple program multiple data environment

Techniques are disclosed for loading programs efficiently in a parallel computing system. In one embodiment, nodes of the parallel computing system receive a load description file which indicates, for each program of a multiple program multiple data (MPMD) job, nodes which are to load the program. The nodes determine, using collective operations, a total number of programs to load and a number of programs to load in parallel. The nodes further generate a class route for each program to be loaded in parallel, where the class route generated for a particular program includes only those nodes on which the program needs to be loaded. For each class route, a node is selected using a collective operation to be a load leader which accesses a file system to load the program associated with a class route and broadcasts the program via the class route to other nodes which require the program.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Collectively loading programs in a multiple program multiple data environment

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Response of a Memristive Biomembrane and Demonstration of Potential Use in Online Learning

The pervasive von Neumann architecture uses complex processor cores and sequential computation. In contrast, the brain is massively parallel and highly efficient, owing to the ability of the neurons and synapses to store and process information simultaneously and to adapt according to incoming information. These features have motivated researchers to develop a host of brain-inspired computers, devices, and models, collectively referred to as neuromorphic computing systems. The quest for synaptic materials capable of closely mimicking biological synapses has led to an alamethicin-doped, synthetic biomembrane with volatile memristive properties which can emulate key synaptic functions to facilitate learning and computation. In contrast to its solid-state counterparts, this two-terminal, biomolecular memristor features similar structure, switching mechanisms, and ionic transport modality as biological synapses while consuming considerably lower power. To use the device as a circuit element, it is important to understand its response to different kinds of input signals. Here we develop a simplified closed form analytical solution based on the underlying state equations for pulse and sine wave inputs. A Verilog-A model based on Runge-Kutta method was developed to incorporate the device in a circuit simulator. Finally, the paper demonstrates possible applications for short- and long-term learning using its unique volatile memristive properties.

Hasan, Md Sakib↗

DOE OSTI2021

hydro-hifem v.1.0

SAND2021-3180 O The hydro-hifem 1.0 software is used to simulate transient physical processes in large geologic environments consisting of complex fractures and man-made infrastructures with affordable computational cost and mesh refinement. The Earth models with such complex model features can be designed by considering the reduction of insignificant dimensions of fractures/infrastructures and embracing their corresponding hierarchical material properties, and their computational meshes are generated by using Cubit. The finite element solutions are automatically distributed across nodes of parallel cluster for efficient computation of transient fluid flow or heat conduction in geologic media. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Beskardes, GungorDidem↗