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At least 1,117 records · Page 62

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Image Gradient Decomposition for Parallel and Memory-Efficient Ptychographic Reconstruction

Ptychography is a popular microscopic imaging modality for many scientific discoveries and sets the record for highest image resolution. Unfortunately, the high image resolution for ptychographic reconstruction requires significant amount of memory and computations, forcing many applications to compromise their image resolution in exchange for a smaller memory footprint and a shorter reconstruction time. In this paper, we propose a novel image gradient decomposition method that significantly reduces the memory footprint for ptychographic reconstruction by tessellating image gradients and diffraction measurements into tiles. In addition, we propose a parallel image gradient decomposition method that enables asynchronous point-to-point communications and parallel pipelining with minimal overhead on a large number of GPUs. Our experiments on a Titanate material dataset (PbTiO3) with 16632 probe locations show that our Gradient Decomposition algorithm reduces memory footprint by 51 times. In addition, it achieves time-to-solution within 2.2 minutes by scaling to 4158 GPUs with a super-linear strong scaling efficiency at 364% compared to runtimes at 6 GPUs. This performance is 2.7 times more memory efficient, 9 times more scalable and 86 times faster than the state-of-the-art algorithm.

Wang, Xiao↗

DOE OSTI2013

Embedding global barrier and collective in torus network with each node combining input from receivers according to class map for output to senders

Embodiments of the invention provide a method, system and computer program product for embedding a global barrier and global interrupt network in a parallel computer system organized as a torus network. The computer system includes a multitude of nodes. In one embodiment, the method comprises taking inputs from a set of receivers of the nodes, dividing the inputs from the receivers into a plurality of classes, combining the inputs of each of the classes to obtain a result, and sending said result to a set of senders of the nodes. Embodiments of the invention provide a method, system and computer program product for embedding a collective network in a parallel computer system organized as a torus network. In one embodiment, the method comprises adding to a torus network a central collective logic to route messages among at least a group of nodes in a tree structure.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Embedding global and collective in a torus network with message class map based tree path selection

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Embedding global barrier and collective in a torus network

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Parallel-in-Time Solution of Scalar Nonlinear Conservation Laws

Here, we consider the parallel-in-time solution of scalar nonlinear conservation laws in one spatial dimension. The equations are discretized in space with a conservative finite-volume method using weighted essentially nonoscillatory (WENO) reconstructions, and in time with high-order explicit Runge–Kutta methods. The solution of the global, discretized space-time problem is sought via a nonlinear iteration that uses a novel linearization strategy in cases of nondifferentiable equations. Under certain choices of discretization and algorithmic parameters, the nonlinear iteration coincides with Newton’s method, although, more generally, it is a preconditioned residual correction scheme. At each nonlinear iteration, the linearized problem takes the form of a certain discretization of a linear conservation law over the space-time domain in question. An approximate parallel-in-time solution of the linearized problem is computed with a single multigrid reduction-in-time (MGRIT) iteration; however, any other effective parallel-in-time method could be used in its place. The MGRIT iteration employs a novel coarse-grid operator that is a modified conservative semi-Lagrangian discretization and generalizes those we have developed previously for nonconservative scalar linear hyperbolic problems. Numerical tests are performed for the inviscid Burgers and Buckley–Leverett equations. For many test problems, the solver converges in just a handful of iterations with a convergence rate independent of mesh resolution, including problems with (interacting) shocks and rarefactions.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

Graphics applications utilizing parallel processing

The results are presented of research conducted to develop a parallel graphic application algorithm to depict the numerical solution of the 1-D wave equation, the vibrating string. The research was conducted on a Flexible Flex/32 multiprocessor and a Sequent Balance 21000 multiprocessor. The wave equation is implemented using the finite difference method. The synchronization issues that arose from the parallel implementation and the strategies used to alleviate the effects of the synchronization overhead are discussed.

Rice, John R.↗

DOE OSTI2018

A Parallel Solver for Graph Laplacians

Problems from graph drawing, spectral clustering, network flow and graph partitioning can all be expressed in terms of graph Laplacian matrices. There are a variety of practical approaches to solving these problems in serial. However, as problem sizes increase and single core speeds stagnate, parallelism is essential to solve such problems quickly. We present an unsmoothed aggregation multigrid method for solving graph Laplacians in a distributed memory setting. We introduce new parallel aggregation and low degree elimination algorithms targeted specifically at irregular degree graphs. These algorithms are expressed in terms of sparse matrix-vector products using generalized sum and product operations. This formulation is amenable to linear algebra using arbitrary distributions and allows us to operate on a 2D sparse matrix distribution, which is necessary for parallel scalability. Our solver outperforms the natural parallel extension of the current state of the art in an algorithmic comparison. We demonstrate scalability to 576 processes and graphs with up to 1.7 billion edges.

Konolige, Tristan↗

DOE OSTI2021

COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients

Background: The COVID-19 pandemic remains a significant global threat. However, despite urgent need, there remains uncertainty surrounding best practices for pharmaceutical interventions to treat COVID-19. In particular, conflicting evidence has emerged surrounding the use of hydroxychloroquine and azithromycin, alone or in combination, for COVID-19. The COVID-19 Evidence Accelerator convened by the Reagan-Udall Foundation for the FDA, in collaboration with Friends of Cancer Research, assembled experts from the health systems research, regulatory science, data science, and epidemiology to participate in a large parallel analysis of different data sets to further explore the effectiveness of these treatments. Methods: Electronic health record (EHR) and claims data were extracted from seven separate databases. Parallel analyses were undertaken on data extracted from each source. Each analysis examined time to mortality in hospitalized patients treated with hydroxychloroquine, azithromycin, and the two in combination as compared to patients not treated with either drug. Cox proportional hazards models were used, and propensity score methods were undertaken to adjust for confounding. Frequencies of adverse events in each treatment group were also examined. Results: Neither hydroxychloroquine nor azithromycin, alone or in combination, were significantly associated with time to mortality among hospitalized COVID-19 patients. No treatment groups appeared to have an elevated risk of adverse events. Conclusion: Administration of hydroxychloroquine, azithromycin, and their combination appeared to have no effect on time to mortality in hospitalized COVID-19 patients. Continued research is needed to clarify best practices surrounding treatment of COVID-19.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Supervised paralled-in-time algorithm for long-time Lagrangian simulations of stochastic dynamics: Application to hydrodynamics

Lagrangian particle methods based on detailed atomic and molecular and nanoscale systems. However, the maximum time step is limited by the smallest oscillation period of the fastest atomic motion, rendering long-time simulations very expensive. To resolve this bottleneck, we propose a supervised parallel-in-time algorithm for stochastic dynamics to accelerate long-time Lagrangian particle simulations. Our method is inspired by bottom-up coarse-graining projections that yield mean-field hydrodynamic behavior in the continuum limit.

Multiscale modeling, Lagrangian method, Parallel-i↗

NASA NTRS1992

Finite element structural analysis and optimization of space frames and trusses in a massively parallel environment

A set of massively parallel computational procedures are formulated to make finite element method based space frame and truss structural response analyses and stochastic method based structural optimization solution superefficient. Several example frame structural analysis and truss optimization problems are presented for demonstration purposes. All calculations are made on the massively parallel environment of CM-2 computer.

Shieh, Rong C.↗

DOE OSTI2018

A massively parallel and memory-efficient FEM toolbox with a hybrid total FETI solver with accelerator support

In this article, we present the ExaScale PaRallel finite element tearing and interconnecting SOlver (ESPRESO) finite element method (FEM) library, which includes an FEM toolbox with interfaces to professional and open-source simulation tools, and a massively parallel hybrid total finite element tearing and interconnecting (HTFETI) solver which can fully utilize the Oak Ridge Leadership Computing Facility Titan supercomputer and achieve superlinear scaling. This article presents several new techniques for finite element tearing and interconnecting (FETI) solvers designed for efficient utilization of supercomputers with a focus on (i) performance—we present a fivefold reduction of solver runtime for the Laplace equation by redesigning the FETI solver and offloading the key workload to the accelerator. We compare Intel Xeon Phi 7120p and Tesla K80 and P100 accelerators to Intel Xeon E5-2680v3 and Xeon Phi 7210 central processing units; and (ii) memory efficiency—we present two techniques which increase the efficiency of the HTFETI solver 1.8 times and push the limits of the largest possible problem ESPRESO that can solve from 124 to 223 billion unknowns for problems with unstructured meshes. Finally, we show that by dynamically tuning hardware parameters, we can reduce energy consumption by up to 33%.

Computer Science↗

NASA NTRS1993

Nonrecursive formulations of multibody dynamics and concurrent multiprocessing

Since the late 1980's, research in recursive formulations of multibody dynamics has flourished. Historically, much of this research can be traced to applications of low dimensionality in mechanism and vehicle dynamics. Indeed, there is little doubt that recursive order N methods are the method of choice for this class of systems. This approach has the advantage that a minimal number of coordinates are utilized, parallelism can be induced for certain system topologies, and the method is of order N computational cost for systems of N rigid bodies. Despite the fact that many authors have dismissed redundant coordinate formulations as being of order N(exp 3), and hence less attractive than recursive formulations, we present recent research that demonstrates that at least three distinct classes of redundant, nonrecursive multibody formulations consistently achieve order N computational cost for systems of rigid and/or flexible bodies. These formulations are as follows: (1) the preconditioned range space formulation; (2) penalty methods; and (3) augmented Lagrangian methods for nonlinear multibody dynamics. The first method can be traced to its foundation in equality constrained quadratic optimization, while the last two methods have been studied extensively in the context of coercive variational boundary value problems in computational mechanics. Until recently, however, they have not been investigated in the context of multibody simulation, and present theoretical questions unique to nonlinear dynamics. All of these nonrecursive methods have additional advantages with respect to recursive order N methods: (1) the formalisms retain the highly desirable order N computational cost; (2) the techniques are amenable to concurrent simulation strategies; (3) the approaches do not depend upon system topology to induce concurrency; and (4) the methods can be derived to balance the computational load automatically on concurrent multiprocessors. In addition to the presentation of the fundamental formulations, this paper presents new theoretical results regarding the rate of convergence of order N constraint stabilization schemes associated with the newly introduced class of methods.

Kurdila, Andrew J.↗

NASA NTRS1997

Visualization of Unsteady Computational Fluid Dynamics

The current compute environment that most researchers are using for the calculation of 3D unsteady Computational Fluid Dynamic (CFD) results is a super-computer class machine. The Massively Parallel Processors (MPP's) such as the 160 node IBM SP2 at NAS and clusters of workstations acting as a single MPP (like NAS's SGI Power-Challenge array and the J90 cluster) provide the required computation bandwidth for CFD calculations of transient problems. If we follow the traditional computational analysis steps for CFD (and we wish to construct an interactive visualizer) we need to be aware of the following: (1) Disk space requirements. A single snap-shot must contain at least the values (primitive variables) stored at the appropriate locations within the mesh. For most simple 3D Euler solvers that means 5 floating point words. Navier-Stokes solutions with turbulence models may contain 7 state-variables. (2) Disk speed vs. Computational speeds. The time required to read the complete solution of a saved time frame from disk is now longer than the compute time for a set number of iterations from an explicit solver. Depending, on the hardware and solver an iteration of an implicit code may also take less time than reading the solution from disk. If one examines the performance improvements in the last decade or two, it is easy to see that depending on disk performance (vs. CPU improvement) may not be the best method for enhancing interactivity. (3) Cluster and Parallel Machine I/O problems. Disk access time is much worse within current parallel machines and cluster of workstations that are acting in concert to solve a single problem. In this case we are not trying to read the volume of data, but are running the solver and the solver outputs the solution. These traditional network interfaces must be used for the file system. (4) Numerics of particle traces. Most visualization tools can work upon a single snap shot of the data but some visualization tools for transient problems require dealing with time.

Haimes, Robert↗

DOE OSTI2016

SU-C-BRC-06: OpenCL-Based Cross-Platform Monte Carlo Simulation Package for Carbon Ion Therapy

Purpose: Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and fundamental physical quantities related to biological effects in carbon ion therapy. Its long computation time impedes clinical and research applications. We have developed an MC package, goCMC, on parallel processing platforms, aiming at achieving accurate and efficient simulations for carbon therapy. Methods: goCMC was developed under OpenCL framework. It supported transport simulation in voxelized geometry with kinetic energy up to 450 MeV/u. Class II condensed history algorithm was employed for charged particle transport with stopping power computed via Bethe-Bloch equation. Secondary electrons were not transported with their energy locally deposited. Energy straggling and multiple scattering were modeled. Production of secondary charged particles from nuclear interactions was implemented based on cross section and yield data from Geant4. They were transported via the condensed history scheme. goCMC supported scoring various quantities of interest e.g. physical dose, particle fluence, spectrum, linear energy transfer, and positron emitting nuclei. Results: goCMC has been benchmarked against Geant4 with different phantoms and beam energies. For 100 MeV/u, 250 MeV/u and 400 MeV/u beams impinging to a water phantom, range difference was 0.03 mm, 0.20 mm and 0.53 mm, and mean dose difference was 0.47%, 0.72% and 0.79%, respectively. goCMC can run on various computing devices. Depending on the beam energy and voxel size, it took 20∼100 seconds to simulate 10{sup 7} carbons on an AMD Radeon GPU card. The corresponding CPU time for Geant4 with the same setup was 60∼100 hours. Conclusion: We have developed an OpenCL-based cross-platform carbon MC simulation package, goCMC. Its accuracy, efficiency and portability make goCMC attractive for research and clinical applications in carbon therapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Communication: A reduced scaling J-engine based reformulation of SOS-MP2 using graphics processing units

We present a low-prefactor, cubically scaling scaled-opposite-spin second-order Møller-Plesset perturbation theory (SOS-MP2) method which is highly suitable for massively parallel architectures like graphics processing units (GPU). The scaling is reduced from O(N{sup 5}) to O(N{sup 3}) by a reformulation of the MP2-expression in the atomic orbital basis via Laplace transformation and the resolution-of-the-identity (RI) approximation of the integrals in combination with efficient sparse algebra for the 3-center integral transformation. In contrast to previous works that employ GPUs for post Hartree-Fock calculations, we do not simply employ GPU-based linear algebra libraries to accelerate the conventional algorithm. Instead, our reformulation allows to replace the rate-determining contraction step with a modified J-engine algorithm, that has been proven to be highly efficient on GPUs. Thus, our SOS-MP2 scheme enables us to treat large molecular systems in an accurate and efficient manner on a single GPU-server.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2010

A Novel Method for Quantifying Helmeted Field of View of a Spacesuit - And What It Means for Constellation

Field of view has always been a design feature paramount to helmet design, and in particular spacesuit design, where the helmet must provide an adequate field of view for a large range of activities, environments, and body positions. Historically, suited field of view has been evaluated either qualitatively in parallel with design or quantitatively using various test methods and protocols. As such, oftentimes legacy suit field of view information is either ambiguous for lack of supporting data or contradictory to other field of view tests performed with different subjects and test methods. This paper serves to document a new field of view testing method that is more reliable and repeatable than its predecessors. It borrows heavily from standard ophthalmologic field of vision tests such as the Goldmann kinetic perimetry test, but is designed specifically for evaluating field of view of a spacesuit helmet. In this test, four suits utilizing three different helmet designs were tested for field of view. Not only do these tests provide more reliable field of view data for legacy and prototype helmet designs, they also provide insight into how helmet design impacts field of view and what this means for the Constellation Project spacesuit helmet, which must meet stringent field of view requirements that are more generous to the crewmember than legacy designs.

McFarland, Shane M.↗

DOE OSTI2014

Segmental Refinement: A Multigrid Technique for Data Locality

We investigate a technique - segmental refinement (SR) - proposed by Brandt in the 1970s as a low memory multigrid method. The technique is attractive for modern computer architectures because it provides high data locality, minimizes network communication, is amenable to loop fusion, and is naturally highly parallel and asynchronous. The network communication minimization property was recognized by Brandt and Diskin in 1994; we continue this work by developing a segmental refinement method for a finite volume discretization of the 3D Laplacian on massively parallel computers. An understanding of the asymptotic complexities, required to maintain textbook multigrid efficiency, are explored experimentally with a simple SR method. A two-level memory model is developed to compare the asymptotic communication complexity of a proposed SR method with traditional parallel multigrid. Performance and scalability are evaluated with a Cray XC30 with up to 64K cores. We achieve modest improvement in scalability from traditional parallel multigrid with a simple SR implementation.

3D Laplacian↗

NASA NTRS2009

A Novel Method for Quantifying Helmeted Field of View of a Space Suit - And What it Means for Constellation

Field of view has always been a design feature paramount to helmet design, and in particular spacesuit design, where the helmet must provide an adequate field of view for a large range of activities, environments, and body positions. Historically, suited field of view has been evaluated either qualitatively in parallel with design or quantitatively using various test methods and protocols. As such, oftentimes legacy suit field of view information is either ambiguous for lack of supporting data or contradictory to other field of view tests performed with different subjects and test methods. This paper serves to document a new field of view testing method that is more reliable and repeatable than its predecessors. It borrows heavily from standard field of vision tests such as the Goldmann kinetic perimetry test, but is designed specifically for evaluating field of view of a spacesuit helmet. In this test, three suits utilizing three different helmet designs were tested for field of view. Not only do these tests provide more reliable field of view data for legacy and prototype helmet designs, they also provide insight into how helmet design impacts field of view and what this means for the Constellation Project spacesuit helmet, which must meet stringent field of view requirements that are more generous to the crewmember than legacy designs.

McFarland, Shane M.↗