Search NASA⌕ Search

SEARCH · Search NASA

Results for “Sparse Matrix Multiplication”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5

Reduce Operations: Send Volume Balancing While Minimizing Latency

Communication hypergraph model was introduced in a two-phase setting for encapsulating multiple communication cost metrics (bandwidth and latency), which are proven to be important in parallelizing irregular applications. In the first phase, computational-task-to-processor assignment is performed with the objective of minimizing total volume while maintaining computational load balance. In the second phase, communication-task-to-processor assignment is performed with the objective of minimizing total number of messages while maintaining communication-volume balance. The reduce-communication hypergraph model suffers from failing to correctly encapsulate send-volume balancing. We propose a novel vertex weighting scheme that enables part weights to correctly encode send-volume loads of processors for send-volume balancing. The model also suffers from increasing the total communication volume during partitioning. To decrease this increase, we propose a method that utilizes the recursive bipartitioning framework and refines each bipartition by vertex swaps. For performance evaluation, we consider column-parallel SpMV, which is one of the most widely known applications in which the reduce-task assignment problem arises. Extensive experiments on 313 matrices show that, compared to the existing model, the proposed models achieve considerable improvements in all communication cost metrics. Furthermore, these improvements lead to an average decrease of 30% in parallel SpMV time on 512 processors for 70 matrices with high irregularity.

97 MATHEMATICS AND COMPUTING↗

FatMan vs. LittleBoy: Scaling Up Linear Algebraic Operations in Scale-Out Data Platforms

Linear algebraic operations such as matrix manipulations form the kernel of many machine learning and other crucial algorithms. Scaling up as well as scaling out such algorithms are highly desirable to enable efficient processing over millions of data points. To this end, we present a matrix manipulation approach to effectively scale-up each node in a scale-out data parallel platform such as Apache Spark. Specifically, we enable hardware acceleration for matrix multiplications in a distributed Spark setup without user intervention. Our approach supports both dense and sparse distributed matrices, and provides flexible control of acceleration by matrix density. We demonstrate the benefit of our approach for generalized matrix multiplication operations over large matrices with up to four billion elements. To connect the effectiveness of our approach with machine learning applications, we performed Gramian matrix computation via generalized matrix multiplications. Our experiments show that our approach achieves more than 2× performance speed-up, and up to 96.1% computation improvement, compared to a state of the art Spark MLlib for dense matrices.

97 MATHEMATICS AND COMPUTING↗

FatMan vs. LittleBoy: Scaling up Linear Algebraic Operations in Scale-out Data Platforms

Linear algebraic operations such as matrix manipulations form the kernel of many machine learning and other crucial algorithms. Scaling up as well as scaling out such algorithms are highly desirable to enable efficient processing over millions of data points. To this end, we present a matrix manipulation approach to effectively scale-up each node in a scale-out data parallel platform such as Apache Spark. Specifically, we enable hardware acceleration for matrix multiplications in a distributed Spark setup without user intervention. Our approach supports both dense and sparse distributed matrices, and provides flexible control of acceleration by matrix density. We demonstrate the benefit of our approach for generalized matrix multiplication operations over large matrices with up to four billion elements. To connect the effectiveness of our approach with machine learning applications, we performed Gramian matrix computation via generalized matrix multiplications. Our experiments show that our approach achieves more than 2x performance speed-up, and up to 96.1% computation improvement, compared to a state of the art Spark MLlib for dense matrices.

Lim, Seung-Hwan↗

SU-G-TeP1-15: Toward a Novel GPU Accelerated Deterministic Solution to the Linear Boltzmann Transport Equation

Purpose: To develop a Graphic Processor Unit (GPU) accelerated deterministic solution to the Linear Boltzmann Transport Equation (LBTE) for accurate dose calculations in radiotherapy (RT). A deterministic solution yields the potential for major speed improvements due to the sparse matrix-vector and vector-vector multiplications and would thus be of benefit to RT. Methods: In order to leverage the massively parallel architecture of GPUs, the first order LBTE was reformulated as a second order self-adjoint equation using the Least Squares Finite Element Method (LSFEM). This produces a symmetric positive-definite matrix which is efficiently solved using a parallelized conjugate gradient (CG) solver. The LSFEM formalism is applied in space, discrete ordinates is applied in angle, and the Multigroup method is applied in energy. The final linear system of equations produced is tightly coupled in space and angle. Our code written in CUDA-C was benchmarked on an Nvidia GeForce TITAN-X GPU against an Intel i7-6700K CPU. A spatial mesh of 30,950 tetrahedral elements was used with an S4 angular approximation. Results: To avoid repeating a full computationally intensive finite element matrix assembly at each Multigroup energy, a novel mapping algorithm was developed which minimized the operations required at each energy. Additionally, a parallelized memory mapping for the kronecker product between the sparse spatial and angular matrices, including Dirichlet boundary conditions, was created. Atomicity is preserved by graph-coloring overlapping nodes into separate kernel launches. The one-time mapping calculations for matrix assembly, kronecker product, and boundary condition application took 452±1ms on GPU. Matrix assembly for 16 energy groups took 556±3s on CPU, and 358±2ms on GPU using the mappings developed. The CG solver took 93±1s on CPU, and 468±2ms on GPU. Conclusion: Three computationally intensive subroutines in deterministically solving the LBTE have been formulated on GPU, resulting in two orders of magnitude speedup. Funding support from Natural Sciences and Engineering Research Council and Alberta Innovates Health Solutions. Dr. Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization).

60 APPLIED LIFE SCIENCES↗

Shifting Between Compute and Memory Bounds: A Compression-Enabled Roofline Model

In the evolving landscape of high-performance computing, especially to fight the end of Moore’s Law and Dennard’s Scaling, the ability to shift between compute-bound and memory-bound states is critical for enhancing adaptability and flexibility to diverse system and domain-specific architectures. Such capability is vital for optimizing performance across distinguished hardware configurations, such as accelerators, memory hierarchies, and cache systems. Despite that ad hoc optimization techniques, such as compressed/approximate computation, have been enabled for compute-/data-intensive computing for improved performance in distinct hardware settings, there lacks an understanding of 1) the rational behind performance improvement; 2) capability of different optimizations; 3) what optimization to respond to specific computational and memory demands. This work proposes a compression-enabled roofline model to facilitate this adaptability with data compression techniques to balance and transform between computational and memory demands. This model enables applications to adjust in response to the specific strengths and limitations of the underlying hardware and system to optimize resource utilization. The effectiveness of this approach is demonstrated with matrix multiplication kernels on different input sizes, with turning on/off various compression techniques, including 1) low-precision floating point; 2) sparse matrix formulation; and 3) compressed arrays with ZFP. By reducing memory transfer volumes and cache misses and increasing data locality and computational intensity through compression, the specific roofline model can transform between compute and memory bounds to align more efficiently with system capabilities. This advancement not only improves overall performance but also maximizes adaptability in diverse computing environments.

Naraparaju, Ramasoumya [University of Washington]↗

Energy-Efficient Neuromorphic Architectures for Nuclear Radiation Detection Applications

A comprehensive analysis and simulation of two memristor-based neuromorphic architectures for nuclear radiation detection is presented. Both scalable architectures retrofit a locally competitive algorithm to solve overcomplete sparse approximation problems by harnessing memristor crossbar execution of vector–matrix multiplications. The proposed systems demonstrate excellent accuracy and throughput while consuming minimal energy for radionuclide detection. To ensure that the simulation results of our proposed hardware are realistic, the memristor parameters are chosen from our own fabricated memristor devices. Based on these results, we conclude that memristor-based computing is the preeminent technology for a radiation detection platform.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

BiGlobal Secondary Instabilities of Roughness-Induced Transient Growth

Roughness-induced transient disturbances distort laminar boundary layers and can lead to premature transition if the roughness is of sufficient height and shape. If transition does occur, it does so through a high-frequency "secondary" instability of the roughness wake. A BiGlobal secondaryinstability code has been developed to solve the stability problem downstream of roughness. The code implements multiple solvers for incompressible/compressible, inviscid/viscous, and temporal/spatial stability. High-order finite differences, sparse matrix linear algebra, LU decomposition, and Arnoldi iterations are used to solve the resulting generalized eigenvalue problem. The code has been used to evaluate the stability properties of experimental roughness-induced transient growth on a flat-plate at low-speed and a slightly blunted cone at M∞= 6. The resulting mode shapes, growth rates, and spatial N-factors show excellent agreement with experimental data. The viscous mode shapes show the best agreement with the experimental disturbance profiles. Yet, execution time can be reduced by an order-of-magnitude by using the inviscid solvers with only modest differences in growth rates.

BiGlobal↗

Why Is Attention Sparse In Particle Transformer?

Transformer-based models have achieved state-of-the-art performance in jet tagging at the CERN Large Hadron Collider (LHC), with the Particle Transformer (ParT) representing a leading example of such models. A striking feature of ParT is its sparse, nearly binary, attention structure, raising questions about the origin of this behavior and whether it encodes physically meaningful correlations. In this work, we investigate the source of ParT's sparse attention by comparing models trained on multiple benchmark datasets and examine the relative contributions of the attention term and the physics-inspired interaction matrix before softmax. We find that binary sparsity arises primarily from the attention mechanism itself, with the interaction matrix playing a secondary role. Moreove, we show that ParT is able to identify key jet substructure elements, such as leptons in semileptonic top decays, even without explicit particle identification inputs. These results provide new insight into the interpretability of transformer-based jet taggers and clarify the conditions under which sparse attention patterns emerge in ParT.

Legge, Timothy [UC, San Diego]↗

Scaling Up Data-Parallel Analytics Platforms: Linear Algebraic Operation Cases

Linear algebraic operations such as matrix manipulations form the kernel of many machine learning and other crucial algorithms. Scaling up as well as scaling out such algorithms are key to supporting large scale data analysis that require efficient processing over millions of data samples. To this end, we present, ARION, a hardware acceleration based approach for scaling-up individual tasks of Spark, a popular data-parallel analytics platform. We support both linear algebraic operations of between two dense matrices, and between sparse and dense matrices in distributed environments. ARION provides a flexible control of acceleration according to matrix density, along with efficient scheduling based on runtime resource utilization. We demonstrate the benefit of our approach for general matrix multiplication operations over large matrices with up to four billion elements by using Gramian matrix computation that is commonly used in machine learning. Experiments show that our approach achieves more than 2× and 1.5× end-to-end performance speedups for dense and sparse matrices, respectively, and up to 57.04× faster computation compared to MLlib, a state of the art Spark-based implementation. This work is sponsored in part by the NSF under the grants: CNS-1565314, CNS-1405697, and CNS-1615411. The manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Xu, Luna↗

Sparse Approximate Multifrontal Factorization with Butterfly Compression for High-Frequency Wave Equations

In this work, we present a fast and approximate multifrontal solver for large-scale sparse linear systems arising from finite-difference, finite-volume or finite-element discretization of high-frequency wave equations. The proposed solver leverages the butterfly algorithm and its hierarchical matrix extension for compressing and factorizing large frontal matrices via graph-distance guided entry evaluation or randomized matrix-vector multiplication-based schemes. Complexity analysis and numerical experiments demonstrate $\mathcal{O}(N\log^2 N)$ computation and $\mathcal{O}(N)$ memory complexity when applied to an $N\times N$ sparse system arising from 3D high-frequency Helmholtz and Maxwell problems.

97 MATHEMATICS AND COMPUTING↗

A graphics processing unit accelerated sparse direct solver and preconditioner with block low rank compression

We present the GPU implementation efforts and challenges of the sparse solver package STRUMPACK. The code is made publicly available on github with a permissive BSD license. STRUMPACK implements an approximate multifrontal solver, a sparse LU factorization which makes use of compression methods to accelerate time to solution and reduce memory usage. Multiple compression schemes based on rank-structured and hierarchical matrix approximations are supported, including hierarchically semi-separable, hierarchically off-diagonal butterfly, and block low rank. Here, in this paper, we present the GPU implementation of the block low rank (BLR) compression method within a multifrontal solver. Our GPU implementation relies on highly optimized vendor libraries such as cuBLAS and cuSOLVER for NVIDIA GPUs, rocBLAS and rocSOLVER for AMD GPUs and the Intel oneAPI Math Kernel Library (oneMKL) for Intel GPUs. Additionally, we rely on external open source libraries such as SLATE (Software for Linear Algebra Targeting Exascale), MAGMA (Matrix Algebra on GPU and Multi-core Architectures), and KBLAS (KAUST BLAS). SLATE is used as a GPU-capable ScaLAPACK replacement. From MAGMA we use variable sized batched dense linear algebra operations such as GEMM, TRSM and LU with partial pivoting. KBLAS provides efficient (batched) low rank matrix compression for NVIDIA GPUs using an adaptive randomized sampling scheme. The resulting sparse solver and preconditioner runs on NVIDIA, AMD and Intel GPUs. Interfaces are available from PETSc, Trilinos and MFEM, or the solver can be used directly in user code. We report results for a range of benchmark applications, using the Perlmutter system from NERSC, Frontier from ORNL, and Aurora from ALCF. For a high frequency wave equation on a regular mesh, using 32 Perlmutter compute nodes, the factorization phase of the exact GPU solver is about 6.5× faster compared to the CPU-only solver. The BLR-enabled GPU solver is about 13.8× faster than the CPU exact solver. For a collection of SuiteSparse matrices, the STRUMPACK exact factorization on a single GPU is on average 1.9× faster than NVIDIA’s cuDSS solver.

97 MATHEMATICS AND COMPUTING↗

A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix

We present an iterative algorithm for computing an invariant subspace associated with the algebraically smallest eigenvalues of a large sparse or structured Hermitian matrix A. We are interested in the case in which the dimension of the invariant subspace is large (e.g., over several hundreds or thousands) even though it may still be small relative to the dimension of A. These problems arise from, for example, density functional theory (DFT) based electronic structure calculations for complex materials. The key feature of our algorithm is that it performs fewer Rayleigh–Ritz calculations compared to existing algorithms such as the locally optimal block preconditioned conjugate gradient or the Davidson algorithm. It is a block algorithm, and hence can take advantage of efficient BLAS3 operations and be implemented with multiple levels of concurrency. We discuss a number of practical issues that must be addressed in order to implement the algorithm efficiently on a high performance computer.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Testing and signal identification for two-sample high-dimensional covariances via multi-level thresholding

The paper considers testing and signal identification for covariance matrices from two populations of marginally sub-Gaussian distributed. A multi-level thresholding procedure is proposed for testing the equality of two high-dimensional covariance matrices, which is designed to detect sparse and faint differences between the covariances. A novel -statistic composition is developed to establish the asymptotic distribution of the thresholding statistics in conjunction with the matrix blocking and the coupling techniques. It is shown that the proposed test is more powerful than the existing tests in detecting sparse and weak signals in covariances. Multiple testing procedures are constructed to discover different covariances and the sub-groups of variables with different covariance structures between the two populations. The proposed procedures are based on the multi-level thresholding test, which are able to control the false discovery proportion () with high power. Simulation experiments and a case study on the returns of the S&P 500 stocks before and after the COVID-19 pandemic are conducted to demonstrate and compare the utilities of the proposed methods.

97 MATHEMATICS AND COMPUTING↗

Extending the eigCG algorithm to nonsymmetric Lanczos for linear systems with multiple right-hand sides

The technique that was used to build the EigCG algorithm for sparse symmetric linear systems is extended to the nonsymmetric case using the BiCG algorithm. We show that, similarly to the symmetric case, we can build an algorithm that is capable of computing a few smallest magnitude eigenvalues and their corresponding left and right eigenvectors of a nonsymmetric matrix using only a small window of the BiCG residuals while simultaneously solving a linear system with that matrix. For a system with multiple right-hand sides, we give an algorithm that computes incrementally more eigenvalues while solving the first few systems and then uses the computed eigenvectors to deflate BiCGStab for the remaining systems. Our experiments on various test problems, including Lattice QCD, show the remarkable ability of EigBiCG to compute spectral approximations with accuracy comparable to that of the unrestarted, nonsymmetric Lanczos. Furthermore, our incremental EigBiCG followed by appropriately restarted and deflated BiCGStab provides a competitive method for systems with multiple right-hand sides.

Abdel-Rehim, A M↗

HyKKT: a hybrid direct-iterative method for solving KKT linear systems

Here, we propose a solution strategy for the large indefinite linear systems arising in interior methods for nonlinear optimization. The method is suitable for implementation on hardware accelerators such as graphical processing units (GPUs). The current gold standard for sparse indefinite systems is the LBLT factorization where L is a lower triangular matrix and B is 1×1 or 2×2 block diagonal. However, this requires pivoting, which substantially increases communication cost and degrades performance on GPUs. Our approach solves a large indefinite system by solving multiple smaller positive definite systems, using an iterative solver on the Schur complement and an inner direct solve (via Cholesky factorization) within each iteration. Cholesky is stable without pivoting, thereby reducing communication and allowing reuse of the symbolic factorization. We demonstrate the practicality of our approach on large optimal power flow problems and show that it can efficiently utilize GPUs and outperform LBL T factorization of the full system.

97 MATHEMATICS AND COMPUTING↗

Computing the Properties of Hadrons, Nuclei, and Nuclear Matter from Quantum Chromodynamics, UNC-CH Final Report.

This is the final technical report for the UNC-CH component of a SciDAC3 project. This project served to coordinate the software development effort which the nuclear physics lattice QCD community is developing to ensure that lattice calculations can make optimal use of forthcoming leadership-class and dedicated hardware, including those of the national laboratories, and prepares for the exploitation of future computational resources in the exascale era. The project developed and optimized simulation software for lattice QCD calculations on leadership class computers and on GPUaccelerated heterogeneous architectures. The participating team at multiple instritutions improved and extended software libraries (Chroma, CPS, MILC, QLUA, QPhiX, QDP++, QDP-jit) by providing interfaces for heterogeneous computing environments and through the optimization of gauge field evolution algorithms and sparse matrix inverters. The former includes the development of new multi-time scale integrators and the latter focused on the development of new multi-grid and domain decomposition inverters for several QCD fermion discretization schemes. The sub-project at the University of North Carolina worked towards the development a domain specific language for lattice QCD computations with the express purpose of generating code with uncompromised performance.

97 MATHEMATICS AND COMPUTING↗

Energy scaling advantages of resistive memory crossbar based computation and its application to sparse coding

In this study, the exponential increase in data over the last decade presents a significant challenge to analytics efforts that seek to process and interpret such data for various applications. Neural-inspired computing approaches are being developed in order to leverage the computational properties of the analog, low-power data processing observed in biological systems. Analog resistive memory crossbars can perform a parallel read or a vector-matrix multiplication as well as a parallel write or a rank-1 update with high computational efficiency. For an N × N crossbar, these two kernels can be O(N) more energy efficient than a conventional digital memory-based architecture. If the read operation is noise limited, the energy to read a column can be independent of the crossbar size (O(1)). These two kernels form the basis of many neuromorphic algorithms such as image, text, and speech recognition. For instance, these kernels can be applied to a neural sparse coding algorithm to give an O(N) reduction in energy for the entire algorithm when run with finite precision. Sparse coding is a rich problem with a host of applications including computer vision, object tracking, and more generally unsupervised learning.

97 MATHEMATICS AND COMPUTING↗

Butterfly Factorization Via Randomized Matrix-Vector Multiplications

This paper presents an adaptive randomized algorithm for computing the butterfly factorization of an m × n matrix with m ≈ n provided that both the matrix and its transpose can be rapidly applied to arbitrary vectors. The resulting factorization is composed of O(log n) sparse factors, each containing O(n) nonzero entries. The factorization can be attained using O(n 3/2 log n) computation and O(n log n) memory resources. Furthermore, the proposed algorithm can be implemented in parallel and can apply to matrices with strong or weak admissibility conditions arising from surface integral equation solvers as well as multi-frontal-based finite-difference, finite-element, or finite-volume solvers. A distributed-memory parallel implementation of the algorithm demonstrates excellent scaling behavior.

97 MATHEMATICS AND COMPUTING↗