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At least 1,441 records · Page 80

All sources NASA NTRS DOE OSTI

DOE OSTI2024

TunIO: An AI-powered Framework for Optimizing HPC I/O

I/O operations are a known performance bottleneck of HPC applications. To achieve good performance, users often employ an iterative multistage tuning process to find an optimal I/O stack configuration. However, an I/O stack contains multiple layers, such as high-level I/O libraries, I/O middleware, and parallel file systems, and each layer has many parameters. These parameters and layers are entangled and influenced by each other. The tuning process is time-consuming and complex. In this work, we present TunIO, an AI-powered I/O tuning framework that implements several techniques to balance the tuning cost and performance gain, including tuning the high-impact parameters first. Furthermore, TunIO analyzes the application source code to extract its I/O kernel while retaining all statements necessary to perform I/O. It utilizes a smart selection of high-impact configuration parameters of the given tuning objective. Finally, it uses a novel Reinforcement Learning (RL)-driven early stopping mechanism to balance the cost and performance gain. Experimental results show that TunIO leads to a reduction of up to ≈73% in tuning time while achieving the same performance gain when compared to H5Tuner. It achieves a significant performance gain/cost of 208.4 MBps/min (I/O bandwidth for each minute spent in tuning) over existing approaches under our testing.

Rajesh, Neeraj↗

DOE OSTI2023

Suppressing Structural Relaxation in Nanoscale Antimony to Enable Ultralow‐Drift Phase‐Change Memory Applications

Abstract Phase‐change random‐access memory (PCRAM) devices suffer from pronounced resistance drift originating from considerable structural relaxation of phase‐change materials (PCMs), which hinders current developments of high‐capacity memory and high‐parallelism computing that both need reliable multibit programming. This work realizes that compositional simplification and geometrical miniaturization of traditional GeSbTe‐like PCMs are feasible routes to suppress relaxation. While to date, the aging mechanisms of the simplest PCM, Sb, at nanoscale, have not yet been unveiled. Here, this work demonstrates that in an optimal thickness of only 4 nm, the thin Sb film can enable a precise multilevel programming with ultralow resistance drift coefficients, in a regime of ≈10 −4 –10 −3 . This advancement is mainly owed to the slightly changed Peierls distortion in Sb and the less‐distorted octahedral‐like atomic configurations across the Sb/SiO 2 interfaces. This work highlights a new indispensable approach, interfacial regulation of nanoscale PCMs, for pursuing ultimately reliable resistance control in aggressively‐miniaturized PCRAM devices, to boost the storage and computing efficiencies substantially.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations

The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers. The results show that DC can speed up the Fock build by 3.0× compared with that of the OTO model. Finally, with similar offloading efforts, DC is a compelling programming model for offloading Fortran applications to GPUs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1977

A system definition study for the Advanced Meteorological Temperature Sounder (AMTS)

The functional requirements of Exhibit A (11) were used as the baseline for the conceptual design of a fixed grating out of plane multidetector spectrometer for the Space Shuttle application. Because the grating instrument would be large and the 28 element detector array would be difficult to cool radiatively from a free flying spacecraft and because increasing the spectral resolution of the grating instrument would be difficult in an instrument of reasonable size, a parallel study of a Nichelson interferometer spectrometer was undertaken. This type of instrument offers compact size, fewer detectors to cool, and the possibility of increased spectral resolution. The design and performance parameters of both the grating and interferometer approaches are described. The tradeoffs involved in comparing the two systems for sounding applications are discussed.

Source record↗

DOE OSTI2024

The inviscid incompressible limit of Kelvin–Helmholtz instability for plasmas

The Kelvin–Helmholtz Instability (KHI) is an interface instability that develops between two fluids or plasmas flowing with a common shear layer. KHI occurs in astrophysical jets, solar atmosphere, solar flows, cometary tails, planetary magnetospheres. Two applications of interest, encompassing both space and fusion applications, drive this study: KHI formation at the outer flanks of the Earth’s magnetosphere and KHI growth from non-uniform laser heating in magnetized direct-drive implosion experiments. Here, we study 2D KHI with or without a magnetic field parallel to the flow. We use both the GAMERA code, which solves the compressible Euler equations, and the STRATOSPEC code, which solves the Navier-Stokes equations under the Boussinesq approximation, coupled with the magnetic field dynamics. GAMERA is a global three-dimensional MHD code with high-order reconstruction in arbitrary nonorthogonal curvilinear coordinates, which is developed for a large range of astrophysical applications. STRATOSPEC is a three-dimensional pseudo-spectral code with an accuracy of infinite order (no numerical diffusion). Magnetized KHI is a canonical case for benchmarking hydrocode simulations with extended MHD options. An objective is to assess whether or not, and under which conditions, the incompressibility hypothesis allows to describe a dynamic compressible system. For comparing both codes, we reach the inviscid incompressible regime, by decreasing the Mach number in GAMERA, and viscosity and diffusion in STRATOSPEC. Here, we specifically investigate both single-mode and multi-mode initial perturbations, either with or without magnetic field parallel to the flow. The method relies on comparisons of the density fields, 1D profiles of physical quantities averaged along the flow direction, and scale-by-scale spectral densities. We also address the triggering, formation and damping of filamentary structures under varying Mach number or Atwood number, with or without a parallel magnetic field. Comparisons show very satisfactory results between the two codes. The vortices dynamics is well reproduced, along with the breaking or damping of small-scale structures. We end with the extraction of growth rates of magnetized KHI from the compressible regime to the incompressible limit in the linear regime assessing the effects of compressibility under increasing magnetic field. The observed differences between the two codes are explained either from diffusion or non-Boussinesq effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Extending OpenSHMEM with Aggregation Support for Improved Message Rate Performance

OpenSHMEM is a highly efficient one-sided communication API that implements the PGAS parallel programming model, and is known for its low latency communication operations that can be mapped efficiently to RDMA capabilities of network interconnects. However, applications that use OpenSHMEM can be sensitive to point-to-point message rates, as many-to-many communication patterns can generate large amounts of small messages which tend to overwhelm network hardware that has predominantly been optimised for bandwidth over message rate. Additionally, many important emerging classes of problems such as data analytics are similarly troublesome for the irregular access patterns they employ. Message aggregation strategies have been proven to significantly enhance network performance, but their implementation often involves complex restructuring of user code, making them unwieldy. This paper shows how to combine the best qualities of message aggregation within the communication model of OpenSHMEM such that applications with small and irregular access patterns can improve network performance while maintaining their algorithmic simplicity. We do this by providing a path to a message aggregation framework called conveyors through a minimally intrusive OpenSHMEM extension introducing aggregation contexts that fit more naturally to the OpenSHMEM atomics, gets, and puts model. We test these extensions using four of the bale 3.0 applications which contain essential many-to-many access patterns to show how they can produce performance improvements of up to 65×.

Welch, Aaron↗

DOE OSTI2021

Entropy production far from equilibrium in a chiral charged plasma in the presence of external electromagnetic fields

We report on the time evolution of a charged strongly coupled N = 4 SYM plasma with an axial anomaly subjected to strong electromagnetic fields. The evolution of this plasma corresponds to a fully backreacted asymptotically AdS 5 solution to the Einstein-Maxwell-Chern-Simons theory. We explore the evolution of the axial current and production of axial charges. As an application we show that after a sufficiently long time both the entropy and the holographic entanglement entropy of a strip-like topology (both parallel to and transverse to the flow of axial current) grow linearly in time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Empirical validation and comparison of methodologies to simulate micro and macro-encapsulated PCMs in the building envelope

Thermal Energy Storage (TES) has the potential to shift peak electricity demand. Passive TES is usually implemented in building envelope as micro and macro encapsulated phase change materials (PCM) to shift electric energy demand and therefore requires careful heat transfer analysis. Whole building energy modelling with simplified heat transfer analysis has become extremely important for designers, architects, engineers, and researchers to predict energy performance of buildings. It is important to validate PCM modelling algorithms used in building energy programs to quantify their error and prove their capacity to model different PCM encapsulation types. This study uses data from a microencapsulated PCM and two macroencapsulated PCMs (Bio based PCM and hydrate salts) tested in full-scale using the Advanced Multiscale Building Energy Research (AMBER) Lab located at the Colorado School of Mines and is used to validate a numerical algorithm written in MATLAB language. To approximate the heat transfer through a wall assembly with macroencapsulated PCM pouches, several modelling techniques that can reduce 3D heat transfer characteristics to 1D are explored in this research. A parallel path heat transfer modelling approach is found to give the closest agreement with the experimental data for the pouched PCMs in building envelope applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Component-wise reduced order model lattice-type structure design

Lattice-type structures can provide a combination of stiffness with light weight that is desirable in a variety of applications. Design optimization of these structures must rely on approximations of the governing physics to render solution of a mathematical model feasible. In this paper, we propose a topology optimization (TO) formulation that approximates the governing physics using component-wise reduced order modeling as introduced in Huynh et al. (2013); Eftang and Patera (2013), which can reduce solution time by multiple orders of magnitude over a full-order finite element model while providing a relative error in the solution of 1%. In addition, the offline training data set from such component-wise models is reusable, allowing its application to many design problems for only the cost of a single offline training phase, and the component-wise method is nearly embarrassingly parallel. We also show how the parameterization chosen in our optimization allows a simplification of the component-wise reduced order model (CWROM) not noted in previous literature, for further speedup of the optimization process. Furthermore, the sensitivity of the compliance with respect to the particular parameterization is derived solely at the component level. In numerical examples, we demonstrate a 1000x speedup over a full-order FEM model with relative error of 1% and show minimum compliance designs for two different cantilever beam examples, one smaller and one larger. Finally, error bounds for the displacement field, compliance, and compliance sensitivity of the CWROM are derived.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Monte-Carlo modeling of phonon thermal transport using DFT-based anisotropic dispersion relations over the full Brillouin zone

In this work, we present a Monte Carlo (MC) approach to solve the phonon Boltzmann transport equation (BTE) in which the anisotropic phonon dispersion relations over the full Brillouin zone (BZ) are used. In this approach, the discretization of the BZ used to compute the phonon relaxation time places constraints on the direction of scattered phonons in the real-space simulation domain. The phonon dispersion and phonon relaxation times are calculated using the density functional theory (DFT) approach. The modified MC approach is validated by a close examination of its ability to simulate phonon transport in both the ballistic and diffusive regimes for multiple materials including GaAs, InAs, ThO 2 , and α-U. In doing so, the phonon thermal conductivities from 100 K to 1000 K are calculated and compared with traditional non-transport solution of the phonon BTE. It is found that the phonon thermal conductivities of α-U and ThO 2 obtained from MC simulations using isotropic dispersion are larger than the values obtained using anisotropic phonon dispersion relations over the full BZ. The effect of phonon-defect scattering on the thermal conductivity of ThO 2 is also studied as an application of the current MC approach and found to agree with previously computed values in the literature. The MC solver developed here has been parallelized as a step to demonstrate its potential to solving computationally intensive phonon thermal transport problems at the mesoscale.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Herbicide, fertilization, and planting density effects on intensively managed loblolly pine early stand development

Production forestry in the southeast US has been partially transitioned to intensively managed short rotations (~10 years), in which multiple silvicultural interventions are performed during forest development. Understanding the responses to silvicultural practices and continued refinement of site-specific recommendations is critical to sustainably maximize forest production. We evaluated the effects of silvicultural practices (herbicide, fertilization, and planting density) on growth, stand homogeneity, and above- and belowground biomass accumulation and partitioning of loblolly pine (Pinus taeda) throughout early stand development (age 5 years) in the southeastern US. Five treatments with eight replications each were tested: no herbicide and no fertilization (C); herbicide only (H); herbicide and half-reduced fertilization rate (R); herbicide and full fertilization (F); and increased stand density (60+ %; 1346 vs. 2152 trees per hectare) with herbicide and full fertilization rate (D). Allometric equations generated from destructive harvests were applied to annual diameter measurements to estimate plot-level biomass and allocation. Herbicide was crucial to promote stand uniformity and increase yield (~600+ % stem biomass compared with C at age 5). Aboveground biomass was similar in R and F treatments, which was ~25% higher than in H at age 5. Increasing planting density along with multiple herbicide and fertilizer applications yielded higher biomass without compromising individual tree size (diameter and height). There was little effect of silviculture practices on allocation patterns. Our results parallel what was found for fertilization with herbicide from a number of loblolly stands under similar conditions and indicate a ~28% volume gain with fertilization during early stand development. Similarly, our results were consistent with other studies implementing similar differences in planting density and suggest a ~26% volume gain through early stand development with an initial 60% increase in planting density. Furthermore, our study helps to understand complex relationships between production and silvicultural practices during early stand development and demonstrates that silvicultural prescriptions can be optimized to increase sustainability of production forestry

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Surrogate Hessian accelerated structural optimization for stochastic electronic structure theories

In this work, we present an efficient energy-based method for structural optimization with stochastic electronic structure theories, such as diffusion quantum Monte Carlo (DMC). This method is based on robust line-search energy minimization in reduced parameter space, exploiting approximate but accurate Hessian information from a surrogate theory, such as density functional theory. The surrogate theory is also used to characterize the potential energy surface, allowing for simple but reliable ways to maximize statistical efficiency while retaining controllable accuracy. We demonstrate the method by finding the minimum DMC energy structures of the selected flake-like aromatic molecules, such as benzene, coronene, and ovalene, represented by 2, 6, and 19 structural parameters, respectively. In each case, the energy minimum is found within two parallel line-search iterations. The method is near-optimal for a line-search technique and suitable for a broad range of applications. It is easily generalized to any electronic structure method where forces and stresses are still under active development and implementation, such as diffusion Monte Carlo, auxiliary-field Monte Carlo, and stochastic configuration interaction, as well as deterministic approaches such as the random-phase approximation. Accurate and efficient means of geometry optimization could shed light on a broad class of materials and molecules, showing high sensitivity of induced properties to structural variables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Engineered bone marrow as a clinically relevant ex vivo model for primary bone cancer research and drug screening

Osteosarcoma (OS) is the most common primary malignant bone cancer in children and adolescents. While numerous other cancers now have promising therapeutic advances, treatment options for OS have remained unchanged since the advent of standard chemotherapeutics and offer less than a 25% 5-y survival rate for those with metastatic disease. This dearth of clinical progress underscores a lack of understanding of OS progression and necessitates the study of this disease in an innovative system. Here, we adapt a previously described engineered bone marrow (eBM) construct for use as a three-dimensional platform to study how microenvironmental and immune factors affect OS tumor progression. We form eBM by implanting acellular bone-forming materials in mice and explanting the cellularized constructs after 8 wk for study. We interrogate the influence of the anatomical implantation site on eBM tissue quality, test ex vivo stability under normoxic (5% O 2 ) and standard (21% O 2 ) culture conditions, culture OS cells within these constructs, and compare them to human OS samples. We show that eBM stably recapitulates the composition of native bone marrow. OS cells exhibit differential behavior dependent on metastatic potential when cultured in eBM, thus mimicking in vivo conditions. Furthermore, we highlight the clinical applicability of eBM as a drug-screening platform through doxorubicin treatment and show that eBM confers a protective effect on OS cells that parallel clinical responses. Combined, this work presents eBM as a cellular construct that mimics the complex bone marrow environment that is useful for mechanistic bone cancer research and drug screening.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Calibr8 v.1.0

Calibr8 provides an application to rapidly prototype and perform material model calibration for complex plasticity models using advanced adjoint or forward sensitivity analyses for execution on massively parallel machines. These techniques can be orders of magnitude faster than traditional finite difference approaches for material model calibration. The underlying technology used in Calibr8 is automatic differentiation, which allows for the rapid implementation and testing of new plasticity models within its framework. Additionally, Calibr8 can perform adjoint-based error estimation to approximate discretization errors for user-implemented plasticity models. 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. SAND2021-10630 O

Granzow, BrianN.↗

DOE OSTI2020

Development of MGMC: A proxy Multi-Group Monte Carlo Particle Transport Application

This document details the development and current state of MGMC: a proxy Multi-Group Monte Carlo transport application. The goal of this work was to develop a light-weight Monte Carlo transport solver that could be easily reconfigured to test parallelization strategies targeting advanced architectures and heterogeneous computing environments. Additionally, MGMC is able to act as a proxy-app for testing the development of algorithms and the integration of other libraries and into Monte Carlo transport codes. MGMC is currently able to run in parallel using OpenMP for CPU threads or CUDA for NVIDIA GPUs. MGMC was also used to investigate the using SYCL for portable parallelization targeting either CPU threads, vender-agnostic GPUs, and ARM chips, detailed in Section II. In the process of developing MGMC, several other C++ libraries have been created with the intent for re-use in future research projects and potential inclusion in production-level codes, detailed in Section III. The physics capabilities in MGMC are detailed in Section IV, code verification is detailed in Section V, and performance results are detailed in Section VI.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

NEAMS-Multiphysics Technical Assistance in FY21

The Multiphysics Object Oriented Simulation Environment (MOOSE) [1] is a massively parallel finite-element/volume package for multiphysics simulation in science and engineering. The package focuses on providing rapid-development capabilities for engineering applications by leveraging well-built features from libMesh [2] and the Portable Extensible Toolkit for Scientific Computation (PETSc) [3]. Fiscal year 2021 (FY-21) was the first year with funding dedicated to supporting MOOSE-derived applications relevant to the Nuclear Engineering Advanced Modeling and Simulation (NEAMS) program. In this report we outline the work done to support NEAMS applications such as BISON, Griffin, Pronghorn, and System Analysis Module (SAM).

42 ENGINEERING↗

DOE OSTI2021

Dynamic Phase Alignment in Inertial Alfven Turbulence

In weakly-collisional plasma environments with sufficiently low electron beta, Alfvenic turbulence transforms into inertial Alfvenic turbulence at scales below the electron skin-depth. We argue that, in inertial Alfvenic turbulence, both energy and generalized kinetic helicity exhibit direct cascades. We demonstrate that the two cascades are compatible due to the existence of a strong scale-dependence of the phase alignment angle between velocity and magnetic field fluctuations, with the phase alignment angle scaling as proportional to the perpendicular wavenumber to the power of -1. The kinetic and magnetic energy spectra scale as the perpendicular wavenumber to the power of -5/3 and -11/3, respectively. As a result of the dual direct cascade, the generalized-helicity spectrum scales as the perpendicular wavenumber to the power of -5/3, implying progressive balancing of the turbulence as the cascade proceeds to smaller scales in the sub-electron-skin-depth range. Turbulent eddies exhibit a phase-space anisotropy, with the parallel wavenumber scaling as the perpendicular wavenumber to the power of 5/3, consistent with critically-balanced inertial Alfven fluctuations. Our results may be applicable to a variety of geophysical, space, and astrophysical environments, including the Earth's magnetosheath and ionosphere, solar corona, non-relativistic pair plasmas, as well as to strongly rotating non-ionized fluids.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1977

Transmission of sound through nonuniform circular ducts with compressible mean flows

An acoustic theory is developed to determine the sound transmission and attenuation through an infinite, hard-walled or lined, circular duct carrying compressible, sheared, mean flows and having a variable cross section. The theory is applicable to large as well as small axial variations, as long as the mean flow does not separate. Although the theory is described for circular ducts, it is applicable to other duct configurations - annular, two dimensional, and rectangular. The theory is described for the linear problem, but the technique is general and has the advantage of being applicable to the nonlinear case as well as the linear case. The technique is based on solving for the envelopes of the quasi-parallel acoustic modes that exist in the duct instead of solving for the actual wave. A computer program was developed. The mean flow model consists of a one dimensional flow in the core and a quarter-sine profile in the boundary layer. Results are presented for the reflection and transmission coefficients in ducts with varying slopes and carrying different mean flows.

Nayfeh, A. H.↗