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Register a new userUnstructured Overlapping Mesh Distribution in Parallel
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Matthew Knepley
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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We present a simple mathematical framework and API for parallel mesh and data distribution, load balancing, and overlap generation. It relies on viewing the mesh as a Hasse diagram, abstracting away information such as cell shape, dimension, and coordinates. The high level of abstraction makes our interface both concise and powerful, as the same algorithm applies to any representable mesh, such as hybrid meshes, meshes embedded in higher dimension, and overlapped meshes in parallel. We present evidence, both theoretical and experimental, that the algorithms are scalable and efficient. A working implementation can be found in the latest release of the PETSc libraries.
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SLEPc is a parallel library for the solution of various types of large-scale eigenvalue problems. In the last years we have been developing a module within SLEPc, called NEP, that is intended for solving nonlinear eigenvalue problems. These problems can be defined by means of a matrix-valued function that depends nonlinearly on a single scalar parameter. We do not consider the particular case of polynomial eigenvalue problems (which are implemented in a different module in SLEPc) and focus here on rational eigenvalue problems and other general nonlinear eigenproblems involving square roots or any other nonlinear function. The paper discusses how the NEP module has been designed to fit the needs of applications and provides a description of the available solvers, including some implementation details such as parallelization. Several test problems coming from real applications are used to evaluate the performance and reliability of the solvers.
In this paper, a parallel structured divide-and-conquer (PSDC) eigensolver is proposed for symmetric tridiagonal matrices based on ScaLAPACK and a parallel structured matrix multiplication algorithm, called PSMMA. Computing the eigenvectors via matrix-matrix multiplications is the most computationally expensive part of the divide-and-conquer algorithm, and one of the matrices involved in such multiplications is a rank-structured Cauchy-like matrix. By exploiting this particular property, PSMMA constructs the local matrices by using generators of Cauchy-like matrices without any communication, and further reduces the computation costs by using a structured low-rank approximation algorithm. Thus, both the communication and computation costs are reduced. Experimental results show that both PSMMA and PSDC are highly scalable and scale to 4096 processes at least. PSDC has better scalability than PHDC that was proposed in [J. Comput. Appl. Math. 344 (2018) 512--520] and only scaled to 300 processes for the same matrices. Comparing with texttt{PDSTEDC} in ScaLAPACK, PSDC is always faster and achieves $1.4$x--$1.6$x speedup for some matrices with few deflations. PSDC is also comparable with ELPA, with PSDC being faster than ELPA when using few processes and a little slower when using many processes.
Sparse matrix-vector multiplication (SpMV) is a central building block for scientific software and graph applications. Recently, heterogeneous processors composed of different types of cores attracted much attention because of their flexible core configuration and high energy efficiency. In this paper, we propose a compressed sparse row (CSR) format based SpMV algorithm utilizing both types of cores in a CPU-GPU heterogeneous processor. We first speculatively execute segmented sum operations on the GPU part of a heterogeneous processor and generate a possibly incorrect results. Then the CPU part of the same chip is triggered to re-arrange the predicted partial sums for a correct resulting vector. On three heterogeneous processors from Intel, AMD and nVidia, using 20 sparse matrices as a benchmark suite, the experimental results show that our method obtains significant performance improvement over the best existing CSR-based SpMV algorithms. The source code of this work is downloadable at https://github.com/bhSPARSE/Benchmark_SpMV_using_CSR
General sparse matrix-matrix multiplication (SpGEMM) is a fundamental building block for numerous applications such as algebraic multigrid method (AMG), breadth first search and shortest path problem. Compared to other sparse BLAS routines, an efficient parallel SpGEMM implementation has to handle extra irregularity from three aspects: (1) the number of nonzero entries in the resulting sparse matrix is unknown in advance, (2) very expensive parallel insert operations at random positions in the resulting sparse matrix dominate the execution time, and (3) load balancing must account for sparse data in both input matrices. In this work we propose a framework for SpGEMM on GPUs and emerging CPU-GPU heterogeneous processors. This framework particularly focuses on the above three problems. Memory pre-allocation for the resulting matrix is organized by a hybrid method that saves a large amount of global memory space and efficiently utilizes the very limited on-chip scratchpad memory. Parallel insert operations of the nonzero entries are implemented through the GPU merge path algorithm that is experimentally found to be the fastest GPU merge approach. Load balancing builds on the number of necessary arithmetic operations on the nonzero entries and is guaranteed in all stages. Compared with the state-of-the-art CPU and GPU SpGEMM methods, our approach delivers excellent absolute performance and relative speedups on various benchmarks multiplying matrices with diverse sparsity structures. Furthermore, on heterogeneous processors, our SpGEMM approach achieves higher throughput by using re-allocatable shared virtual memory. The source code of this work is available at https://github.com/bhSPARSE/Benchmark_SpGEMM_using_CSR
Sparse matrix-vector multiplication (SpMV) is a fundamental building block for numerous applications. In this paper, we propose CSR5 (Compressed Sparse Row 5), a new storage format, which offers high-throughput SpMV on various platforms including CPUs, GPUs and Xeon Phi. First, the CSR5 format is insensitive to the sparsity structure of the input matrix. Thus the single format can support an SpMV algorithm that is efficient both for regular matrices and for irregular matrices. Furthermore, we show that the overhead of the format conversion from the CSR to the CSR5 can be as low as the cost of a few SpMV operations. We compare the CSR5-based SpMV algorithm with 11 state-of-the-art formats and algorithms on four mainstream processors using 14 regular and 10 irregular matrices as a benchmark suite. For the 14 regular matrices in the suite, we achieve comparable or better performance over the previous work. For the 10 irregular matrices, the CSR5 obtains average performance improvement of 17.6%, 28.5%, 173.0% and 293.3% (up to 213.3%, 153.6%, 405.1% and 943.3%) over the best existing work on dual-socket Intel CPUs, an nVidia GPU, an AMD GPU and an Intel Xeon Phi, respectively. For real-world applications such as a solver with only tens of iterations, the CSR5 format can be more practical because of its low-overhead for format conversion. The source code of this work is downloadable at https://github.com/bhSPARSE/Benchmark_SpMV_using_CSR5
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