A bibliography on parallel and vector numerical algorithms

This is a bibliography of numerical methods. It also includes a number of other references on machine architecture, programming language, and other topics of interest to scientific computing. Certain conference proceedings and anthologies which have been published in book form are listed also

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed

Evaluating the Impact of SDC on the GMRES Iterative Solver

Increasing parallelism and transistor density, along with increasingly tighter energy and peak power constraints, may force exposure of occasionally incorrect computation or storage to application codes. Silent data corruption (SDC) will likely be infrequent, yet one SDC suffices to make numerical algorithms like iterative linear solvers cease progress towards the correct answer. Thus, we focus on resilience of the iterative linear solver GMRES to a single transient SDC. We derive inexpensive checks to detect the effects of an SDC in GMRES that work for a more general SDC model than presuming a bit flip. Our experiments show that when GMRES is used as the inner solver of an inner-outer iteration, it can "run through" SDC of almost any magnitude in the computationally intensive orthogonalization phase. That is, it gets the right answer using faulty data without any required roll back. Those SDCs which it cannot run through, get caught by our detection scheme

ELSI: A Unified Software Interface for Kohn-Sham Electronic Structure Solvers

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.Comment: 55 pages, 14 figures, 2 table

Improvements in sparse matrix operations of NASTRAN

A "nontransmit" packing routine was added to NASTRAN to allow matrix data to be refered to directly from the input/output buffer. Use of the packing routine permits various routines for matrix handling to perform a direct reference to the input/output buffer if data addresses have once been received. The packing routine offers a buffer by buffer backspace feature for efficient backspacing in sequential access. Unlike a conventional backspacing that needs twice back record for a single read of one record (one column), this feature omits overlapping of READ operation and back record. It eliminates the necessity of writing, in decomposition of a symmetric matrix, of a portion of the matrix to its upper triangular matrix from the last to the first columns of the symmetric matrix, thus saving time for generating the upper triangular matrix. Only a lower triangular matrix must be written onto the secondary storage device, bringing 10 to 30% reduction in use of the disk space of the storage device

Sparse approximate inverse preconditioners on high performance GPU platforms

Simulation with models based on partial differential equations often requires the solution of (sequences of) large and sparse algebraic linear systems. In multidimensional domains, preconditioned Krylov iterative solvers are often appropriate for these duties. Therefore, the search for efficient preconditioners for Krylov subspace methods is a crucial theme. Recent developments, especially in computing hardware, have renewed the interest in approximate inverse preconditioners in factorized form, because their application during the solution process can be more efficient. We present here some experiences focused on the approximate inverse preconditioners proposed by Benzi and Tůma from 1996 and the sparsification and inversion proposed by van Duin in 1999. Computational costs, reorderings and implementation issues are considered both on conventional and innovative computing architectures like Graphics Programming Units (GPUs)

Evaluation of Directive-Based GPU Programming Models on a Block Eigensolver with Consideration of Large Sparse Matrices

Achieving high performance and performance portability for large-scale scientific applications is a major challenge on heterogeneous computing systems such as many-core CPUs and accelerators like GPUs. In this work, we implement a widely used block eigensolver, Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG), using two popular directive based programming models (OpenMP and OpenACC) for GPU-accelerated systems. Our work differs from existing work in that it adopts a holistic approach that optimizes the full solver performance rather than narrowing the problem into small kernels (e.g., SpMM, SpMV). Our LOPBCG GPU implementation achieves a 2.8$${\times }$$–4.3$${\times }$$ speedup over an optimized CPU implementation when tested with four different input matrices. The evaluated configuration compared one Skylake CPU to one Skylake CPU and one NVIDIA V100 GPU. Our OpenMP and OpenACC LOBPCG GPU implementations gave nearly identical performance. We also consider how to create an efficient LOBPCG solver that can solve problems larger than GPU memory capacity. To this end, we create microbenchmarks representing the two dominant kernels (inner product and SpMM kernel) in LOBPCG and then evaluate performance when using two different programming approaches: tiling the kernels, and using Unified Memory with the original kernels. Our tiled SpMM implementation achieves a 2.9$${\times }$$ and 48.2$${\times }$$ speedup over the Unified Memory implementation on supercomputers with PCIe Gen3 and NVLink 2.0 CPU to GPU interconnects, respectively