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At least 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

m-CUBES An efficient and portable implementation of multi-dimensional integration for gpus

The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation. Multi-dimensional integration is often time-prohibitive on CPUs. Efficient implementation on many-core architectures is challenging as the workload across the integration space cannot be predicted a priori. We propose m-Cubes, a novel implementation of the well-known Vegas algorithm for execution on GPUs. Vegas transforms integration variables followed by calculation of a Monte Carlo integral estimate using adaptive partitioning of the resulting space. m-Cubes improves performance on GPUs by maintaining relatively uniform workload across the processors. As a result, our optimized Cuda implementation for Nvidia GPUs outperforms parallelization approaches proposed in past literature. We further demonstrate the efficiency of m-Cubes by evaluating a six-dimensional integral from a cosmology application, achieving significant speedup and greater precision than the CUBA library's CPU implementation of VEGAS. We also evaluate m-Cubes on a standard integrand test suite. m-Cubes outperforms the serial implementations of the Cuba and GSL libraries by orders of magnitude speedup while maintaining comparable accuracy. Our approach yields a speedup of at least 10 when compared against publicly available Monte Carlo based GPU implementations. In summary, m-Cubes can solve integrals that are prohibitively expensive using standard libraries and custom implementations. A modern C++ interface header-only implementation makes m-Cubes portable, allowing its utilization in complicated pipelines with easy to define stateful integrals. Compatibility with non-Nvidia GPUs is achieved with our initial implementation of m-Cubes using the Kokkos framework.

Sakiotis, Ioannis↗
DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important features of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Analysis of Monte Carlo accelerated iterative methods for sparse linear systems: Analysis of Monte Carlo accelerated iterative methods for sparse linear systems

Here, we consider hybrid deterministic-stochastic iterative algorithms for the solution of large, sparse linear systems. Starting from a convergent splitting of the coefficient matrix, we analyze various types of Monte Carlo acceleration schemes applied to the original preconditioned Richardson (stationary) iteration. We expect that these methods will have considerable potential for resiliency to faults when implemented on massively parallel machines. We also establish sufficient conditions for the convergence of the hybrid schemes, and we investigate different types of preconditioners including sparse approximate inverses. Numerical experiments on linear systems arising from the discretization of partial differential equations are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Sparse Binary Matrix-Vector Multiplication on Neuromorphic Computers

Neuromorphic computers offer the opportunity for low-power, efficient computation. Though they have been primarily applied to neural network tasks, there is also the opportunity to leverage the inherent characteristics of neuromorphic computers (low power, massive parallelism, collocated processing and memory) to perform non-neural network tasks. Here, we demonstrate how an approach for performing sparse binary matrix-vector multiplication on neuromorphic computers. We describe the approach, which relies on the connection between binary matrix-vector multiplication and breadth first search, and we introduce the algorithm for performing this calculation in a neuromorphic way. We validate the approach in simulation. Finally, we provide a discussion of the runtime of this algorithm and discuss where neuromorphic computers in the future may have a computational advantage when performing this computation.

Schuman, Catherine↗
DOE OSTI2023

A Surrogate-Based Asynchronous Decomposition Technique for Realistic Security-Constrained Optimal Power Flow Problems

Here we present a decomposition approach for obtaining good feasible solutions for the security-constrained, alternating-current, optimal power flow (SC-AC-OPF) problem at an industrial scale and under real-world time and computational limits. The approach was designed while preparing and participating in ARPA-E’s Grid Optimization Competition (GOC) Challenge 1. The challenge focused on a near-real-time version of the SC-AC-OPF problem, where a base operating point is optimized, taking into account possible single-element contingencies, after which the system adapts its operating point following the response of automatic frequency droop controllers and voltage regulators. Our solution approach for this problem relies on state-of-the-art nonlinear programming algorithms, and it employs nonconvex relaxations for complementarity constraints, a specialized two-stage decomposition technique with sparse approximations of recourse terms and contingency ranking and prescreening. The paper describes and justifies our approach and outlines the features of its implementation, including functions and derivatives evaluation, warm-starting strategies, and asynchronous parallelism. We discuss the results of the independent benchmark of our approach by ARPA-E’s GOC team in Challenge 1, where it was found to consistently produce high-quality solutions across a wide range of network sizes and difficulty, and conclude by outlining future extensions of the approach.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Targeting tissues via dynamic human systems modeling in generative design

Drug discovery is a complex, costly process with high failure rates. A successful drug should bind to a target, be deliverable to an intended site of activity, and promote a desired pharmacological effect without causing toxicity. Typically, these factors are evaluated in series over the course of a pipeline where the number of candidates is sequentially whittled down from a very large initial pool. One promise of AI-driven discovery is the opportunity to evaluate multiple facets of drug performance in parallel. However, despite ML-driven advancements, current models for pharmacological property prediction are exclusively trained to predict molecular properties, ignoring important, dynamic biodistribution and bioactivity effects. Here, we present our progress towards incorporating quantitative systems physiology models into an AI-enabled drug design and molecular generation pipeline. Within a genetic algorithm, we include human-relevant physiologically based pharmacokinetic (PBPK) models. These PBPK models leverage properties that are predicted by a fine-tuned molecular language model. Together, these models will aid in capturing the mapping between molecules and therapeutic outcomes that is necessary to accelerate the drug discovery process.

Fox, Zach↗
DOE OSTI2026

Two-Tower Quantum Matrix Chain Multiplication: Trading Qubits for Depth

Matrix chain multiplication -- computing $\mathcal{W} = M^{(0)}\cdots M^{(K-1)}$ where $M^{(k)} \in \mathbb{R}^{P_k \times P_{k+1}}$-- arises in scientific computing, machine learning, and graph analysis. Despite the importance of this problem, for chains of distinct matrices, the classical number of operations grows linearly with the chain length $K$ and polynomially in the matrix dimensions. We present \emph{Two-Tower Matrix Multiplication}, a quantum subroutine that encodes the product $\mathcal{W}$ of the $K$ matrices into a quantum state in circuit depth $\mathcal{O}(\max_{k} \mathrm{polylog} (P_k P_{k+1}))$, which is independent of~$K$ within the QRAM-based state-preparation model, whereas the qubit count is $\mathcal{O}\bigl(\sum_{k} \log P_k \bigr)$; the total gate count remains linear in $K$, so the gain is in the circuit depth. The construction interleaves state-preparation operators across two layers; within each layer, all operators act on disjoint registers and execute in parallel. This subroutine can be specialized for the chain-vector case, which computes the product of $K-1$ matrices applied to a vector. We prove the correctness of the subroutine for all $K$ and provide two implementations using the Qiskit and QCLAB frameworks. The subroutine is applicable to any downstream quantum algorithm that operates on a matrix encoded in the statevector, including norm estimation, graph-matrix powers, linear system solving, and quantum machine learning kernels.

Antonioli, Giacomo [Pisa U.] (ORCID:00090000668703↗
DOE OSTI2017

Multigroup Monte Carlo on GPUs: Comparison of history- and event-based algorithms

This article presents an investigation of the performance of different multigroup Monte Carlo transport algorithms on GPUs with a discussion of both history-based and event-based approaches. Several algorithmic improvements are introduced for both approaches. By modifying the history-based algorithm that is traditionally favored in CPU-based MC codes to occasionally filter out dead particles to reduce thread divergence, performance exceeds that of either the pure history-based or event-based approaches. The impacts of several algorithmic choices are discussed, including performance studies on Kepler and Pascal generation NVIDIA GPUs for fixed source and eigenvalue calculations. Single-device performance equivalent to 20–40 CPU cores on the K40 GPU and 60–80 CPU cores on the P100 GPU is achieved. Last, in addition, nearly perfect multi-device parallel weak scaling is demonstrated on more than 16,000 nodes of the Titan supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Institute for Sustained Performance, Energy, and Resilience (SuPER)

The University of Tennessee (UTK) and University of Texas at El Paso (UTEP) partnership supported the three main thrusts of the SUPER project---performance, energy, and resilience. The UTK-UTEP effort thus helped advance the main goal of SUPER, which was to ensure that DOE's computational scientists can successfully exploit the emerging generation of high performance computing (HPC) systems. This goal is being met by providing application scientists with strategies and tools to productively maximize performance, conserve energy, and attain resilience. The primary vehicle through which UTK provided performance measurement support to SUPER and the larger HPC community is the Performance Application Programming Interface (PAPI). PAPI is an ongoing project that provides a consistent interface and methodology for collecting hardware performance information from various hardware and software components, including most major CPUs, GPUs and accelerators, interconnects, I/O systems, and power interfaces, as well as virtual cloud environments. The PAPI software is widely used for performance modeling of scientific and engineering applications---for example, the HOMME (High Order Methods Modeling Environment) climate code, and the GAMESS and NWChem computational chemistry codes---on DOE supercomputers. PAPI is widely deployed as middleware for use by higher-level profiling, tracing, and sampling tools (e.g., CrayPat, HPCToolkit, Scalasca, Score-P, TAU, Vampir, PerfExpert), making it the de facto standard for hardware counter analysis. PAPI has established itself as fundamental software infrastructure in every application domain (spanning academia, government, and industry), where improving performance can be mission critical. Ultimately, as more application scientists migrate their applications to HPC platforms, they will benefit from the extended capabilities this grant brought to PAPI to analyze and optimize performance in these environments, whether they use PAPI directly, or via third-party performance tools. Capabilities added to PAPI through this grant include support for new architectures such as the lastest GPU and Xeon Phi accelerators, and advanced power measurement and management features. Another important topic for the UTK team was providing support for a rich ecosystem of different fault management strategies in the context of parallel computing. Our long term efforts have been oriented toward proposing flexible strategies and providing building boxes that application developers can use to build the most efficient fault management technique for their application. These efforts span across the entire software spectrum, from theoretical models of existing strategies to easily assess their performance, to algorithmic modifications to take advantage of specific mathematical properties for data redundancy and to extensions to widely used programming paradigms to empower the application developers to deal with all types of faults. We have also continued our tight collaborations with users to help them adopt these technologies to ensure their application always deliver meaningful scientific data. Large supercomputer systems are becoming more and more power and energy constrained, and future systems and applications running on them will need to be optimized to run under power caps and/or minimize energy consumption. The UTEP team contributed to the SUPER energy thrust by developing power modeling methodologies and investigating power management strategies. Scalability modeling results showed that some applications can scale better with respect to an increasing power budget than with respect to only the number of processors. Power management, in particular shifting power to processors on the critical path of an application execution, can reduce perturbation due to system noise and other sources of runtime variability, which are growing problems on large-scale power-constrained computer systems.

42 ENGINEERING↗
DOE OSTI2016

CRUNCH_PARALLEL

The code CRUNCH_PARALLEL is a parallel version of the CRUNCH code. CRUNCH code version 2.0 was previously released by LLNL, (UCRL-CODE-200063). Crunch is a general purpose reactive transport code developed by Carl Steefel and Yabusake (Steefel Yabsaki 1996). The code handles non-isothermal transport and reaction in one, two, and three dimensions. The reaction algorithm is generic in form, handling an arbitrary number of aqueous and surface complexation as well as mineral dissolution/precipitation. A standardized database is used containing thermodynamic and kinetic data. The code includes advective, dispersive, and diffusive transport.

Shumaker, Dana E.↗
DOE OSTI2026

Generalized Power Flow Model of an Extra High-Power Multi-Terminal HVdc Transmission Grid with Parallel-Connected and Voltage-Stacked Converters

To increase power transfer capacity of high-voltage direct current (HVdc) transmission, a new extra high-power HVdc architecture with multiple standard modular multilevel converters (MMCs) per substation has recently been introduced. This paper proposes a power flow model for a multi-terminal HVdc (MTdc) grid with this innovative substation architecture. The proposed MTdc model can be integrated seamlessly with existing ac-dc power flow algorithms with minimal modifications. The model is applicable to various MTdc grid types and topologies, different numbers of dc buses, dc lines, and MMCs per substation, along with diverse control parameters. In addition, it accurately captures both balanced and unbalanced operations of the MTdc grid. The proposed model is verified using a 5-terminal bipole MTdc grid that spans 4 areas in the Eastern Interconnection system of the USA. The numerical solutions obtained from unified and sequential ac-dc power flow algorithms under different operating conditions closely match the time-domain simulation results in PSCAD, validating the accuracy and versatility of the proposed MTdc power flow model.

Nguyen, Quan H.↗
DOE OSTI2014

PETSc Users Manual (Rev. 3.4)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself; For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

PETSc Users Manual (Rev. 3.5)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear, nonlinear equation solvers and time integrators that may be used in application codes written in Fortran, C, C++, Python, and MATLAB (sequential). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++ or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. ;For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. PETSc also has a MATLAB interface, so portions of your code can be written in MATLAB to “try out” the PETSc solvers. The resulting code will not be scalable however because currently MATLAB is inherently not scalable; and PETSc should not be used to attempt to provide a “parallel linear solver” in an otherwise sequential code. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect any kind of reasonable performance. Do not expect to generate your matrix sequentially and then “use PETSc” to solve the linear system in parallel. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc is supported; see the web site http://www.mcs.anl.gov/petsc for information on contacting support. A http://www.mcs.anl.gov/petsc/publications may be found a list of publications and web sites that feature work involving PETSc. We welcome any reports of corrections for this document.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Development and Benchmarking of a Hybrid PIC Code For Dense Plasmas and Fast Ignition (Final Report)

Radiation processes play an important role in the study of both fast ignition and other inertial confinement schemes, such as plasma jet driven magneto-inertial fusion, both in their effect on energy balance, and in generating diagnostic signals. In the latter case, warm and hot dense matter may be produced by the convergence of a plasma shell formed by the merging of an assembly of high Mach number plasma jets. This innovative approach has the potential advantage of creating matter of high energy densities in voluminous amount compared with high power lasers or particle beams. An important application of this technology is as a plasma liner for the flux compression of magnetized plasma to create ultra-high magnetic fields and burning plasmas. HyperV Technologies Corp. has been developing plasma jet accelerator technology in both coaxial and linear railgun geometries to produce plasma jets of sufficient mass, density, and velocity to create such imploding plasma liners. An enabling tool for the development of this technology is the ability to model the plasma dynamics, not only in the accelerators themselves, but also in the resulting magnetized target plasma and within the merging/interacting plasma jets during transport to the target. Welch pioneered numerical modeling of such plasmas (including for fast ignition) using the LSP simulation code. Lsp is an electromagnetic, parallelized, plasma simulation code under development since 1995. It has a number of innovative features making it uniquely suitable for modeling high energy density plasmas including a hybrid fluid model for electrons that allows electrons in dense plasmas to be modeled with a kinetic or fluid treatment as appropriate. In addition to in-house use at Voss Scientific, several groups carrying out research in Fast Ignition (LLNL, SNL, UCSD, AWE (UK), and Imperial College (UK)) also use LSP. A collaborative team consisting of HyperV Technologies Corp., Voss Scientific LLC, FAR-TECH, Inc., Prism Computational Sciences, Inc. and Advanced Energy Systems Inc. joined efforts to develop new physics and numerical models for LSP in several key areas to enhance the ability of LSP to model high energy density plasmas (HEDP). This final report details those efforts. Areas addressed in this research effort include: adding radiation transport to LSP, first in 2D and then fully 3D, extending the EMHD model to 3D, implementing more advanced radiation and electrode plasma boundary conditions, and installing more efficient implicit numerical algorithms to speed complex 2-D and 3-D computations. The new capabilities allow modeling of the dominant processes in high energy density plasmas, and further assist the development and optimization of plasma jet accelerators, with particular attention to MHD instabilities and plasma/wall interaction (based on physical models for ion drag friction and ablation/erosion of the electrodes). In the first funding cycle we implemented a solver for the radiation diffusion equation. To solve this equation in 2-D, we used finite-differencing and applied the parallelized sparse-matrix solvers in the PETSc library (Argonne National Laboratory) to the resulting system of equations. A database of the necessary coefficients for materials of interest was assembled using the PROPACEOS and ATBASE codes from Prism. The model was benchmarked against Prism's 1-D radiation hydrodynamics code HELIOS, and against experimental data obtained from HyperV's separately funded plasma jet accelerator development program. Work in the second funding cycle focused on extending the radiation diffusion model to full 3-D, continued development of the EMHD model, optimizing the direct-implicit model to speed up calculations, add in multiply ionized atoms, and improved the way boundary conditions are handled in LSP. These new LSP capabilities were then used, along with analytic calculations and Mach2 runs, to investigate plasma jet merging, plasma detachment and transport, restrike and advanced jet accelerator design. In addition, a strong linkage to diagnostic measurements was made by modeling plasma jet experiments on PLX to support benchmarking of the code. A large number of upgrades and improvements advancing hybrid PIC algorithms were implemented in LSP during the second funding cycle. These include development of fully 3D radiation transport algorithms, new boundary conditions for plasma-electrode interactions, and a charge conserving equation of state that permits multiply ionized high-Z ions. The final funding cycle focused on 1) mitigating the effects of a slow-growing grid instability which is most pronounced in plasma jet frame expansion problems using the two-fluid Eulerian remap algorithm, 2) extension of the Eulerian Smoothing Algorithm to allow EOS/Radiation modeling, 3) simulations of collisionless shocks formed by jet merging, 4) simulations of merging jets using high-Z gases, 5) generation of PROPACEOS EOS/Opacity databases, 6) simulations of plasma jet transport experiments, 7) simulations of plasma jet penetration through transverse magnetic fields, and 8) GPU PIC code development. The tools developed during this project are applicable not only to the study of plasma jets, but also to a wide variety of HEDP plasmas of interest to DOE, including plasmas created in short-pulse laser experiments performed to study fast ignition concepts for inertial confinement fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Grouper: A Compact, Streamable Triangle Mesh Data Structure

Here, we present Grouper: an all-in-one compact file format, random-access data structure, and streamable representation for large triangle meshes. Similarly to the recently published SQuad representation, Grouper represents the geometry and connectivity of a mesh by grouping vertices and triangles into fixed-size records, most of which store two adjacent triangles and a shared vertex. Unlike SQuad, however, Grouper interleaves geometry with connectivity and uses a new connectivity representation to ensure that vertices and triangles can be stored in a coherent order that enables memory-efficient sequential stream processing. We also present a linear-time construction algorithm that allows streaming out Grouper meshes using a small memory footprint while preserving the initial ordering of vertices. In this construction, we show how the problem of assigning vertices and triangles to groups reduces to a well-known NP-hard optimization problem, and present a simple yet effective heuristic solution that performs well in practice. Our array-based Grouper representation also doubles as a triangle mesh data structure that allows direct access to vertices and triangles. Storing only about two integer references per triangle-i.e., less than the three vertex references stored with each triangle in a conventional indexed mesh format-Grouper answers both incidence and adjacency queries in amortized constant time. Our compact representation enables data-parallel processing on multicore computers, instant partitioning and fast transmission for distributed processing, as well as efficient out-of-core access. We demonstrate the versatility and performance benefits of Grouper using a suite of example meshes and processing kernels.

97 MATHEMATICS AND COMPUTING↗