The thesis presents usefulness of duality between graph and his adjacency matrix. The teoretical part provides the basis of graph theory and matrix algebra mainly focusing on sparse matrices and options of their presentation witch takes into account the number of nonzero elements in the matrix. The thesis includes presentation of possible operations on sparse matrices and algorithms that basically work on graphs, but with help of duality between graph and his adjacency matrix can be presented with sequence of operations on matrices.
Practical part presents implementation of some algorithms that can work both with graphs or their adjacency matrices in programming language Java and testing algorithms that work with matrices.
It focuses on comparison in efficiency of algorithm working with matrix written in standard mode and with matrix written in format for sparse matrices. It also studies witch presentation of matrices works beter for witch algorithm.

Graph algorithms in the language of linear algebra

Wilkinson defined a sparse matrix as one with enough zeros that it pays to take advantage of them.1 This informal yet practical definition captures the essence of the goal of direct methods for solving sparse matrix problems. They exploit the sparsity of a matrix to solve problems economically: much faster and using far less memory than if all the entries of a matrix were stored and took part in explicit computations. These methods form the backbone of a wide range of problems in computational science. A glimpse of the breadth of applications relying on sparse solvers can be seen in the origins of matrices in published matrix benchmark collections (Duff and Reid 1979a, Duff, Grimes and Lewis 1989a, Davis and Hu 2011). The goal of this survey article is to impart a working knowledge of the underlying theory and practice of sparse direct methods for solving linear systems and least-squares problems, and to provide an overview of the algorithms, data structures, and software available to solve these problems, so that the reader can both understand the methods and know how best to use them.

A survey of direct methods for sparse linear systems

This timely text presents a comprehensive overview of fault tolerance techniques for high-performance computing (HPC). The text opens with a detailed introduction to the concepts of checkpoint protocols and scheduling algorithms, prediction, replication, silent error detection and correction, together with some application-specific techniques such as ABFT. Emphasis is placed on analytical performance models. This is then followed by a review of general-purpose techniques, including several checkpoint and rollback recovery protocols. Relevant execution scenarios are also evaluated and compared through quantitative models. Features: provides a survey of resilience methods and performance models; examines the various sources for errors and faults in large-scale systems; reviews the spectrum of techniques that can be applied to design a fault-tolerant MPI; investigates different approaches to replication; discusses the challenge of energy consumption of fault-tolerance methods in extreme-scale systems.

/pdf/fault-tolerance-techniques-for-high-performance-computing-28z1e6yekc.pdf

Fault-Tolerance Techniques for High-Performance Computing

Autotuning refers to the automatic generation of a search space of possible implementations of a computation that are evaluated through models and/or empirical measurement to identify the most desirable implementation. Autotuning has the potential to dramatically improve the performance portability of petascale and exascale applications. To date, autotuning has been used primarily in high-performance applications through tunable libraries or previously tuned application code that is integrated directly into the application. This paper draws on the authors’ extensive experience applying autotuning to high-performance applications, describing both successes and future challenges. If autotuning is to be widely used in the HPC community, researchers must address the software engineering challenges, manage configuration overheads, and continue to demonstrate significant performance gains and portability across architectures. In particular, tools that configure the application must be integrated into the application build process so that tuning can be reapplied as the application and target architectures evolve.

Autotuning in High-Performance Computing Applications

We present a fast algorithm for kernel summation problems in high dimensions. Such problems appear in computational physics, numerical approximation, nonparametric statistics, and machine learning. In our context, the sums depend on a kernel function that is a pair potential defined on a dataset of points in a high-dimensional Euclidean space. A direct evaluation of the sum scales quadratically with the number of points. Fast kernel summation methods can reduce this cost to linear complexity, but the constants involved do not scale well with the dimensionality of the dataset. The main algorithmic components of fast kernel summation algorithms are the separation of the kernel sum between near and far field (which is the basis for pruning) and the efficient and accurate approximation of the far field. We introduce novel methods for pruning and for approximating the far field. Our far field approximation requires only kernel evaluations and does not use analytic expansions. Pruning is not done using bounding...

Askit: approximate skeletonization kernel-independent treecode in high dimensions ∗

We show how to use the idea of self-stabilization, which originates in the context of distributed control, to make fault-tolerant iterative solvers. Generally, a self-stabilizing system is one that, starting from an arbitrary state (valid or invalid), reaches a valid state within a finite number of steps. This property imbues the system with a natural means of tolerating transient faults. We give two proof-of-concept examples of self-stabilizing iterative linear solvers: one for steepest descent (SD) and one for conjugate gradients (CG). Our self-stabilized versions of SD and CG require small amounts of fault-detection, e.g., we may check only for NaNs and infinities. We test our approach experimentally by analyzing its convergence and overhead for different types and rates of faults. Beyond the specific findings of this paper, we believe self-stabilization has promise to become a useful tool for constructing resilient solvers more generally.

https://hpcgarage.org/pmaa2014/slides.pdf

Self-stabilizing iterative solvers

This paper presents the first hybrid MPI+OpenMP+CUDA implementation of a distributed memory right-looking unsymmetric sparse direct solver (i.e., sparse LU factorization) that uses static pivoting. While BLAS calls can account for more than 40% of the overall factorization time, the difficulty is that small problem sizes dominate the workload, making efficient GPU utilization challenging. This fact motivates our approach, which is to find ways to aggregate collections of small BLAS operations into larger ones; to schedule operations to achieve load balance and hide long-latency operations, such as PCIe transfer; and to exploit simultaneously all of a node’s available CPU cores and GPUs.

/pdf/a-distributed-cpu-gpu-sparse-direct-solver-5coxt8zi35.pdf

A Distributed CPU-GPU Sparse Direct Solver

Due to the limited capacity of GPU memory, the majority of prior work on graph applications on GPUs has been restricted to graphs of modest sizes that fit in memory. Recent hardware and software advances make it possible to address much larger host memory transparently as a part of a feature known as unified virtual memory. While accessing host memory over an interconnect is understandably slower, the problem space has not been sufficiently explored in the context of a challenging workload with low computational intensity and an irregular data access pattern such as graph traversal. We analyse the performance of breadth first search (BFS) for several large graphs in the context of unified memory and identify the key factors that contribute to slowdowns. Next, we propose a lightweight offline graph reordering algorithm, HALO (Harmonic Locality Ordering), that can be used as a pre-processing step for static graphs. HALO yields speedups of 1.5x-1.9x over baseline in subsequent traversals. Our method specifically aims to cover large directed real world graphs in addition to undirected graphs whereas prior methods only account for the latter. Additionally, we demonstrate ties between the locality ordering problem and graph compression and show that prior methods from graph compression such as recursive graph bisection can be suitably adapted to this problem.

/pdf/traversing-large-graphs-on-gpus-with-unified-memory-13h6t4sq3l.pdf

Traversing large graphs on GPUs with unified memory

We propose a new algorithm to improve the strong scalability of right-looking sparse LU factorization on distributed memory systems. Our 3D sparse LU algorithm uses a three-dimensional MPI process grid, aggressively exploits elimination tree parallelism and trades off increased memory for reduced per-process communication. We also analyze the asymptotic improvements for planar graphs (e.g., from 2D grid or mesh domains) and certain non-planar graphs (specifically for 3D grids and meshes). For planar graphs with n vertices, our algorithm reduces communication volume asymptotically in n by a factor of O{log n} and latency by a factor of O{log n}. For non-planar cases, our algorithm can reduce the per-process communication volume by 3× and latency by O{n^1/3} times. In all cases, the memory needed to achieve these gains is a constant factor. We implemented our algorithm by extending the 2D data structure used in superLU. Our new 3D code achieves speedups up to 27× for planar graphs and up to 3.3× for non-planar graphs over the baseline 2D superLU when run on 24,000 cores of a Cray XC30.

A Communication-Avoiding 3D LU Factorization Algorithm for Sparse Matrices

We show how to exploit graph sparsity in the Floyd-Warshall algorithm for the all-pairs shortest path (Apsp) problem. Floyd-Warshall is an attractive choice for Apsp on high-performing systems due to its structural similarity to solving dense linear systems and matrix multiplication. However, if sparsity of the input graph is not properly exploited, Floyd-Warshall will perform unnecessary asymptotic work and thus may not be a suitable choice for many input graphs. To overcome this limitation, the key idea in our approach is to use the known algebraic relationship between Floyd-Warshall and Gaussian elimination, and import several algorithmic techniques from sparse Cholesky factorization, namely, fill-in reducing ordering, symbolic analysis, supernodal traversal, and elimination tree parallelism. When combined, these techniques reduce computation, improve locality and enhance parallelism. We implement these ideas in an efficient shared memory parallel prototype that is orders of magnitude faster than an efficient multi-threaded baseline Floyd-Warshall that does not exploit sparsity. Our experiments suggest that the Floyd-Warshall algorithm can compete with Dijkstra's algorithm (the algorithmic core of Johnson's algorithm) for several classes sparse graphs.

https://dl.acm.org/doi/pdf/10.1145/3332466.3374533

Piyush Sao

Papers

Self-stabilizing iterative solvers

A Distributed CPU-GPU Sparse Direct Solver

Traversing large graphs on GPUs with unified memory

A Communication-Avoiding 3D LU Factorization Algorithm for Sparse Matrices

A supernodal all-pairs shortest path algorithm