Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

Preconditioning complex symmetric linear systems

A new polynomial preconditioner for symmetric complex linear systems based on Hermitian and skew-Hermitian splitting (HSS) for complex symmetric linear systems is herein presented. It applies to Conjugate Orthogonal Conjugate Gradient (COCG) or Conjugate Orthogonal Conjugate Residual (COCR) iterative solvers and does not require any estimation of the spectrum of the coefficient matrix. An upper bound of the condition number of the preconditioned linear system is provided. Moreover, to reduce the computational cost, an inexact variant based on incomplete Cholesky decomposition or orthogonal polynomials is proposed. Numerical results show that the present preconditioner and its inexact variant are efficient and robust solvers for this class of linear systems. A stability analysis of the method completes the description of the preconditioner.Comment: 26 pages, 4 figures, 4 table

Four-dimensional tomographic reconstruction by time domain decomposition

Since the beginnings of tomography, the requirement that the sample does not change during the acquisition of one tomographic rotation is unchanged. We derived and successfully implemented a tomographic reconstruction method which relaxes this decades-old requirement of static samples. In the presented method, dynamic tomographic data sets are decomposed in the temporal domain using basis functions and deploying an L1 regularization technique where the penalty factor is taken for spatial and temporal derivatives. We implemented the iterative algorithm for solving the regularization problem on modern GPU systems to demonstrate its practical use

A comparison of numerical splitting-based methods for Markovian dependability and performability models

Iterative numerical methods are an important ingredient for the solution of continuous time Markov dependability models of fault-tolerant systems. In this paper we make a numerical comparison of several splitting-based iterative methods. We consider the computation of steady-state reward rate on rewarded models. This measure requires the solution of a singular linear system. We consider two classes of models. The first class includes failure/repair models. The second class is more general and includes the modeling of periodic preventive test of spare components to reduce the probability of latent failures in inactive components. The periodic preventive test is approximated by an Erlang distribution with enough number of stages. We show that for each class of model there is a splitting-based method which is significantly more efficient than the other methods.Postprint (published version

A rational deferred correction approach to parabolic optimal control problems

The accurate and efficient solution of time-dependent PDE-constrained optimization problems is a challenging task, in large part due to the very high dimension of the matrix systems that need to be solved. We devise a new deferred correction method for coupled systems of time-dependent PDEs, allowing one to iteratively improve the accuracy of low-order time stepping schemes. We consider two variants of our method, a splitting and a coupling version, and analyze their convergence properties. We then test our approach on a number of PDE-constrained optimization problems. We obtain solution accuracies far superior to that achieved when solving a single discretized problem, in particular in cases where the accuracy is limited by the time discretization. Our approach allows for the direct reuse of existing solvers for the resulting matrix systems, as well as state-of-the-art preconditioning strategies