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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Unified Communication Optimization Strategies for Sparse Triangular Solver on CPU and GPU Clusters

This paper presents a unified communication optimization framework for sparse triangular solve (SpTRSV) algorithms on CPU and GPU clusters. The framework builds upon a 3D communication-avoiding (CA) layout of Px × Py × Pz processes that divides a sparse matrix into Pz submatrices, each handled by a Px × Py 2D grid with block-cyclic distribution. We propose three communication optimization strategies: First, a new 3D SpTRSV algorithm is developed, which trades the inter-grid communication and synchronization with replicated computation. This design requires only one inter-grid synchronization, and the inter-grid communication is efficiently implemented with sparse allreduce operations. Second, broadcast and reduction communication trees are used to reduce message latency of the intra-grid 2D communication on CPU clusters. Finally, we leverage GPU-initiated one-sided communication to implement the communication trees on GPU clusters. With these nested inter- and intra-grid communication optimization strategies, the proposed 3D SpTRSV algorithm can attain up to 3.45x speedups compared to the baseline 3D SpTRSV algorithm using up to 2048 Cori Haswell CPU cores. In addition, the proposed GPU 3D SpTRSV algorithm can achieve up to 6.5x speedups compared to the proposed CPU 3D SpTRSV algorithm with Pz up to 64. Finally it is remarkable that the proposed GPU 3D SpTRSV can scale to 256 GPUs using the Perlmutter system while the existing 2D SpTRSV algorithm can only scale up to 4 GPUs.

Sao, Piyush↗
DOE OSTI2016

Educating local radial basis functions using the highest gradient of interest in three dimensional geometries: EDUCATING LOCALIZED RBF-SCHEMES

We present a novel methodology to effectively localize radial basis function approximation methods in three dimensions. The local scheme requires shape parameter-dependent functions that can be used to approximate gradients of scattered data and to solve partial differential operators. The optimum shape parameter is obtained from the highest gradient of interest, where a known analytical function, when boundary conditions are not present, or a shape parameter-free global approximation are used to educate the localized scheme. The later option is applicable to problems where the operator needs to be solved multiple times, like in time evolution or stochastic integration. Past shape parameter's optimizations, for two-dimensional domains, based on the condition number of the interpolant matrix, were unable to provide satisfactory approximations. The applicability of our method is illustrated in the context of an analytical expression interpolation and during a Ginzburg-Landau relaxation of a free energy functional. In general, the optimum shape parameter depends on geometry, node distribution, and density, whereas the approximation errors decrease as the node density and the local stencil size increase. The effective localization of radial basis functions motivates its use in moving boundary problems and accelerates solutions through sparse matrix solvers.

free energy functional↗
DOE OSTI2023

Improved quantum algorithms for linear and nonlinear differential equations

We present substantially generalized and improved quantum algorithms over prior work for inhomogeneous linear and nonlinear ordinary differential equations (ODE). Specifically, we show how the norm of the matrix exponential characterizes the run time of quantum algorithms for linear ODEs opening the door to an application to a wider class of linear and nonlinear ODEs. In [1], a quantum algorithm for a certain class of linear ODEs is given, where the matrix involved needs to be diagonalizable. The quantum algorithm for linear ODEs presented here extends to many classes of non-diagonalizable matrices including singular matrices. The algorithm here is also exponentially faster than the bounds derived in [1] for certain classes of diagonalizable matrices. Our linear ODE algorithm is then applied to nonlinear differential equations using Carleman linearization (an approach taken recently by us in [2]). The improvement over that result is two-fold. First, we obtain an exponentially better dependence on error. This kind of logarithmic dependence on error has also been achieved by [3], but only for homogeneous nonlinear equations. Second, the present algorithm can handle any sparse matrix (that models dissipation) if it has a negative log-norm (including non-diagonalizable matrices), whereas [2] and [3] additionally require normality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

MATAR: A performance portability and productivity implementation of data-oriented design with Kokkos

There is a need for simple, fast, and memory-efficient multidimensional data structures for dense and sparse storage that arise with numerical methods and in software applications. The data structures must perform equally well across multiple computer architectures, including CPUs and GPUs. For this purpose, we developed MATAR, a C++ software library that allows for simple creation and use of intricate data structures that is also portable across disparate architectures using Kokkos. Here, the performance aspect is achieved by forcing contiguous memory layout (or as close to contiguous as possible) for multidimensional and multi-size dense or sparse MATrix and ARray (hence, MATAR) types. Our results show that MATAR has the capability to improve memory utilization, performance, and programmer productivity in scientific computing. This is achieved by fitting more work into the available memory, minimizing memory loads required, and by loading memory in the most efficient order. This document describes the purpose of the work, the implementation of each of the data types, and the resulting performance both in some simple baseline test cases and in an application code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Porting DMRG++ Scientific Application to OpenPOWER

With the rapidly changing microprocessor designs and architectural diversity (multi-cores, many-cores, accelerators) for the next generation HPC systems, scientific applications must adapt to the hardware, to exploit the different types of parallelism and resources available in the architecture. To get the benefit of all the in-node hardware threads, it is important to use a single programming model to map and coordinate the available work to the different heterogeneous execution units in the node (e.g., multi-core hardware threads (latency optimized), accelerators (bandwidth optimized), etc.).Our goal is to show that we can manage the node complexity of these systems by using OpenMP for in-node parallelization by exploiting different “programming styles” supported by OpenMP 4.5 to program CPU cores and accelerators. Finding out the suitable programming-style (e.g., SPMD style, multi-level tasks, accelerator programming, nested parallelism, or a combination of these) using the latest features of OpenMP to maximize performance and achieve performance portability across heterogeneous and homogeneous systems is still an open research problem.We developed a mini-application, Kronecker Product (KP), from the original DMRG++ application (sparse matrix algebra) computational motif to experiment with different OpenMP programming styles on an OpenPOWER architecture and present their results in this paper.

Chatterjee, Ronnie↗
DOE OSTI2017

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolution in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Optimizing shift selection in multilevel Monte Carlo for disconnected diagrams in lattice QCD

The calculation of disconnected diagram contributions to physical signals is a computationally expensive task in Lattice QCD. To extract the physical signal, the trace of the inverse Lattice Dirac operator, a large sparse matrix, must be stochastically estimated. Because the variance of the stochastic estimator is typically large, variance reduction techniques must be employed. Multilevel Monte Carlo (MLMC) methods reduce the variance of the trace estimator by utilizing a telescoping sequence of estimators. Frequency Splitting is one such method that uses a sequence of inverses of shifted operators to estimate the trace of the inverse lattice Dirac operator, however there is no a priori way to select the shifts that minimize the cost of the multilevel trace estimation. Here we present a sampling and interpolation scheme that is able to predict the variances associated with Frequency Splitting under displacements of the underlying space time lattice. The interpolation scheme is able to predict the variances to high accuracy and therefore chooses shifts that correspond to an approximate minimum of the cost for the trace estimation. We show that Frequency Splitting with the chosen shifts displays significant speedups over multigrid deflation, and that these shifts can be used for multiple configurations within the same ensemble with no penalty to performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Basker: Parallel sparse LU factorization utilizing hierarchical parallelism and data layouts

Transient simulation in circuit simulation tools, such as SPICE and Xyce, depend on scalable and robust sparse LU factorizations for efficient numerical simulation of circuits and power grids. As the need for simulations of very large circuits grow, the prevalence of multicore architectures enable us to use shared memory parallel algorithms for such simulations. A parallel factorization is a critical component of such shared memory parallel simulations. We develop a parallel sparse factorization algorithm that can solve problems from circuit simulations efficiently, and map well to architectural features. This new factorization algorithm exposes hierarchical parallelism to accommodate irregular structure that arise in our target problems. It also uses a hierarchical two-dimensional data layout which reduces synchronization costs and maps to memory hierarchy found in multicore processors. We present an OpenMP based implementation of the parallel algorithm in a new multithreaded solver called Basker in the Trilinos framework. Here, we present performance evaluations of Basker on the Intel SandyBridge and Xeon Phi platforms using circuit and power grid matrices taken from the University of Florida sparse matrix collection and from Xyce circuit simulation. Basker achieves a geometric mean speedup of 5.91× on CPU (16 cores) and 7.4× on Xeon Phi (32 cores) relative to state-of-the-art solver KLU. Basker outperforms Intel MKL Pardiso solver (PMKL) by as much as 30× on CPU (16 cores) and 7.5× on Xeon Phi (32 cores) for low fill-in circuit matrices. Furthermore, Basker provides 5.4× speedup on a challenging matrix sequence taken from an actual Xyce simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring

Metabolomics has a long history of using cosine similarity to match experimental tandem mass spectra to databases for compound identification. Here we introduce the Blur-and-Link (BLINK) approach for scoring cosine similarity. By bypassing fragment alignment and simultaneously scoring all pairs of spectra using sparse matrix operations, BLINK is over 3000 times faster than MatchMS, a widely used loop-based alignment and scoring implementation. Using a similarity cutoff of 0.7, BLINK and MatchMS had practically equivalent identification agreement, and greater than 99% of their scores and matching ion counts were identical. This performance improvement can enable calculations to be performed that would typically be limited by time and available computational resources.

47 OTHER INSTRUMENTATION↗
DOE OSTI2015

Modeling optical properties of silicon clusters by first principles: From a few atoms to large nanocrystals

Time dependent density functional tight binding (TDDFTB) method is implemented with sparse matrix techniques and improved parallelization algorithms. The method is employed to calculate the optical properties of various Si nanocrystals (NCs). The calculated light absorption spectra of small Si NCs from TDDFTB were found to be comparable with many body perturbation methods utilizing planewave basis sets. For large Si NCs (more than a thousand atoms) that are beyond the reach of conventional approaches, the TDDFTB method is able to produce reasonable results that are consistent with prior experiments. We also employed the method to study the effects of surface chemistry on the optical properties of large Si NCs. We learned that the optical properties of Si NCs can be manipulated with small molecule passivations such as methyl, hydroxyl, amino, and fluorine. In general, the shifts and profiles in the absorption spectra can be tuned with suitably chosen passivants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Real-space solution to the electronic structure problem for nearly a million electrons

We report a Kohn–Sham density functional theory calculation of a system with more than 200 000 atoms and 800 000 electrons using a real-space high-order finite-difference method to investigate the electronic structure of large spherical silicon nanoclusters. Our system of choice was a 20 nm large spherical nanocluster with 202 617 silicon atoms and 13 836 hydrogen atoms used to passivate the dangling surface bonds. To speed up the convergence of the eigenspace, we utilized Chebyshev-filtered subspace iteration, and for sparse matrix–vector multiplications, we used blockwise Hilbert space-filling curves, implemented in the PARSEC code. For this calculation, we also replaced our orthonormalization + Rayleigh–Ritz step with a generalized eigenvalue problem step. We utilized all of the 8192 nodes (458 752 processors) on the Frontera machine at the Texas Advanced Computing Center. We achieved two Chebyshev-filtered subspace iterations, yielding a good approximation of the electronic density of states. Our work pushes the limits on the capabilities of the current electronic structure solvers to nearly 106 electrons and demonstrates the potential of the real-space approach to efficiently parallelize large calculations on modern high-performance computing platforms.

Chemistry↗
DOE OSTI2026

Detector alignment for X-ray crystallography using Millepede-II

I describe a method for accurately refining the geometrical parameters of segmented X-ray area detectors on the basis of serial crystallography data, using 'Millepede' – an algorithm created for a very similar problem in high-energy physics. The Millepede method for serial crystallography builds on the approach of Brewster et al. [Acta Cryst. (2018), D74, 877–894], in which the detector parameters are refined simultaneously with the parameters for each individual crystal. This accounts for the mutual dependency between the parameters and thereby avoids the bias and slow convergence problems that have afflicted older approaches in which the deviations between observed and calculated Bragg peak positions were taken directly as the updates for the detector panel positions. The Millepede method uses the special structure of the least-squares normal equations to reduce them to a much smaller form that can be solved very quickly, even compared with the sparse matrix methods used previously. This makes it practical to refine the detector geometry frequently and thereby maintain accurate calibration without specialized alignment campaigns. Tilts of detector panels out of the plane can be reliably refined, as can the overall distance of the detector in the beam direction. With a simulated test case, the new method produced panel shifts within 7% of the correct values with only one iteration, and produced almost exactly correct shifts after a second iteration. A simulated out-of-plane panel rotation was correctly determined to within 0.001°. Applied to experimental data from an X-ray free-electron laser, the method increased the indexable fraction of frames from 30% to 91% in a single iteration, and to 96% after two further iterations. Computing the geometry updates on the basis of 2060 crystals took only 0.819 s on desktop computing hardware, including the time taken to read the required data from disk. The scaling was found to be very close to linear for up to 100 980 sets of crystal parameters, which took only 78.2 s to process under the same conditions. The method has been applied as part of a real-time feedback system at a synchrotron radiation beamline, in which an out-of-plane detector tilt of 0.04° was detected and corrected. Possible further applications are also described here.

Millepede-II↗
DOE OSTI2017

Architecture Independent Integrated Early Performance and Energy Estimation

The end of Dennard’s scaling, coupled to the necessity to keep increasing computational performance in constrained power envelopes, is leading developers towards the need to opti- mize applications not only for performance, but also for energy consumption. In such a scenario, solutions that enable estimating performance and energy consumption of a program as early as possible, even during development and without the necessity to access the final target hardware, can become fundamental tools to reduce the design space, the optimization effort, and provide potential opportunities to automate the optimization process itself. In this position paper, we discuss the design of a performance and energy estimation framework based on a retargetable com- piler. Our proposed approach targets the Intermediate Repre- sentation (IR) of the LLVM compiler. The IR based approach enables, after a model is built, estimation from a host different from the target architecture, even considering dynamic infor- mation. We present the rationale behind such a framework, identify opportunities and components readily available (such as the provided static analysis, quick ways to add instrumentation for dynamic profiling, and the multiple backends), and aspects that still need further research efforts (such as more effective non-linear, or machine learning based models). We also discuss a hand-developed case study, based on a simple sparse matrix vector multiplication with a linear model, to motivate the needs for such a framework.

Estimation, Compilers, Performance Analysis↗
DOE OSTI2015

Parallel implementation and performance optimization of the configuration-interaction method

The configuration-interaction (CI) method, long a popular approach to describe quantum many-body systems, is cast as a very large sparse matrix eigenpair problem with matrices whose dimension can exceed one billion. Such formulations place high demands on memory capacity and memory bandwidth - - two quantities at a premium today. In this paper, we describe an efficient, scalable implementation, BIGSTICK, which, by factorizing both the basis and the interaction into two levels, can reconstruct the nonzero matrix elements on the fly, reduce the memory requirements by one or two orders of magnitude, and enable researchers to trade reduced resources for increased computational time. We optimize BIGSTICK on two leading HPC platforms - - the Cray XC30 and the IBM Blue Gene/Q. Specifically, we not only develop an empirically-driven load balancing strategy that can evenly distribute the matrix-vector multiplication across 256K threads, we also developed techniques that improve the performance of the Lanczos reorthogonalization. Combined, these optimizations improved performance by 1.3-8× depending on platform and configuration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Brief Announcement: Communication Optimal Sparse LU Factorization for Planar Matrices

We introduce a new parallel algorithm for solving sparse LU factorization of planar matrices, which commonly arise in the finite element method for 2D PDEs. Existing scalable methods, such as the multifrontal approach with subtree-to-subcube mapping by Gupta et al. [1] and right-looking with 3D mapping by Sao et al. [2] fail to achieve optimal communication costs for these matrices. Our new algorithm combines 3D mapping and subtree-to-subcube mapping to minimize communication costs while allowing trade-offs between extra memory and reduced communication. We demonstrate that our proposed algorithm attains the communication lower bound up to a factor of O(log log n) in the memory-optimal case and up to a factor of O(log P) in the memory-independent case for an n-dimensional planar sparse matrix on P processors.

Sao, Piyush↗
DOE OSTI2022

Fast Sparse-Vector Cosine Similarity in Go

This software provides a fast way to perform efficient sparse matrix multiplication followed by top-n multiplication result selection. Functionality for performing matrix multiplication / cosine similarity separately is included in this package as well. This package is a pure Go port of a Python package developed by ING Bank (https://github.com/ing-bank/sparse_dot_topn) which uses Cython to execute the matrix multiplication in C++. Instructions for compiling bindings which can be called from Python are included with this package as well.

Shivers, Ryan [Oak Ridge National Lab. (ORNL), Oak↗
DOE OSTI2022

Tacho

SAND2022-7470 O Tacho is a performance portable sparse direct solver for use with various sparse matrix problems which typically arise from finite element methods. The code relies on the Kokkos parallel programming model porting to both CPUs and GPUs. It is also part of the Trilinos library. 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.

Kim, Kyungjoo↗