X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/GMRES2stage.git/blobdiff_plain/fd0a7d17543c653d442bccd0c7ee035764e83650..8fb4ff584e40d579fbf8019ec98eda27c2f877f0:/paper.tex diff --git a/paper.tex b/paper.tex index e23ccc2..8f469bd 100644 --- a/paper.tex +++ b/paper.tex @@ -439,7 +439,7 @@ can be around 7 times faster. \end{abstract} \begin{IEEEkeywords} -Iterative Krylov methods; sparse linear systems; error minimization; PETSc; %à voir... +Iterative Krylov methods; sparse linear systems; residual minimization; PETSc; %à voir... \end{IEEEkeywords} @@ -583,10 +583,10 @@ performances. The present paper is organized as follows. In Section~\ref{sec:02} some related works are presented. Section~\ref{sec:03} presents our two-stage algorithm using a least-square residual minimization. Section~\ref{sec:04} describes some -convergence results on this method. Section~\ref{sec:05} shows some -experimental results obtained on large clusters of our algorithm using routines -of PETSc toolkit. Finally Section~\ref{sec:06} concludes and gives some -perspectives. +convergence results on this method. In Section~\ref{sec:05}, parallization +details of TSARM are given. Section~\ref{sec:06} shows some experimental +results obtained on large clusters of our algorithm using routines of PETSc +toolkit. Finally Section~\ref{sec:06} concludes and gives some perspectives. %%%********************************************************* %%%********************************************************* @@ -604,7 +604,7 @@ perspectives. %%%********************************************************* %%%********************************************************* -\section{A Krylov two-stage algorithm} +\section{Two-stage algorithm with least-square residuals minimization} \label{sec:03} A two-stage algorithm is proposed to solve large sparse linear systems of the form $Ax=b$, where $A\in\mathbb{R}^{n\times n}$ is a sparse and square @@ -613,58 +613,72 @@ $b\in\mathbb{R}^n$ is the right-hand side. The algorithm is implemented as an inner-outer iteration solver based on iterative Krylov methods. The main key points of our solver are given in Algorithm~\ref{algo:01}. -In order to accelerate the convergence, the outer iteration is implemented as an -iterative Krylov method which minimizes some error functions over a Krylov -subspace~\cite{saad96}. At each iteration, the sparse linear system $Ax=b$ is -solved iteratively with an iterative method, for example GMRES -method~\cite{saad86} or some of its variants, and the Krylov subspace that we -used is spanned by a basis $S$ composed of successive solutions issued from the -inner iteration -\begin{equation} - S = \{x^1, x^2, \ldots, x^s\} \text{,~} s\leq n. -\end{equation} -The advantage of such a Krylov subspace is that we neither need an orthogonal -basis nor any synchronization between processors to generate this basis. The -algorithm is periodically restarted every $s$ iterations with a new initial -guess $x=S\alpha$ which minimizes the residual norm $\|b-Ax\|_2$ over the Krylov -subspace spanned by vectors of $S$, where $\alpha$ is a solution of the normal -equations -\begin{equation} - R^TR\alpha = R^Tb, -\end{equation} -which is associated with the least-squares problem +In order to accelerate the convergence, the outer iteration periodically applies +a least-square minimization on the residuals computed by the inner solver. The +inner solver is a Krylov based solver which does not required to be changed. + +At each outer iteration, the sparse linear system $Ax=b$ is solved, only for $m$ +iterations, using an iterative method restarting with the previous solution. For +example, the GMRES method~\cite{Saad86} or some of its variants can be used as a +inner solver. The current solution of the Krylov method is saved inside a matrix +$S$ composed of successive solutions computed by the inner iteration. + +Periodically, every $s$ iterations, the minimization step is applied in order to +compute a new solution $x$. For that, the previous residuals are computed with +$(b-AS)$. The minimization of the residuals is obtained by \begin{equation} \underset{\alpha\in\mathbb{R}^{s}}{min}\|b-R\alpha\|_2 \label{eq:01} \end{equation} -such that $R=AS$ is a dense rectangular matrix in $\mathbb{R}^{n\times s}$, -$s\ll n$, and $R^T$ denotes the transpose of matrix $R$. We use an iterative -method to solve the least-squares problem~(\ref{eq:01}) such as CGLS -~\cite{hestenes52} or LSQR~\cite{paige82} which are more appropriate than a -direct method in the parallel context. +with $R=AS$. Then the new solution $x$ is computed with $x=S\alpha$. + + +In practice, $R$ is a dense rectangular matrix in $\mathbb{R}^{n\times s}$, +$s\ll n$. In order to minimize~(\ref{eq:01}), a least-square method such as +CGLS ~\cite{Hestenes52} or LSQR~\cite{Paige82} is used. Those methods are more +appropriate than a direct method in a parallel context. \begin{algorithm}[t] -\caption{A Krylov two-stage algorithm} +\caption{TSARM} \begin{algorithmic}[1] \Input $A$ (sparse matrix), $b$ (right-hand side) \Output $x$ (solution vector)\vspace{0.2cm} \State Set the initial guess $x^0$ - \For {$k=1,2,3,\ldots$ until convergence} \label{algo:conv} - \State Solve iteratively $Ax^k=b$ \label{algo:solve} - \State $S_{k~mod~s}=x^k$ - \If {$k$ mod $s=0$ {\bf and} not convergence} - \State Compute dense matrix $R=AS$ - \State Solve least-squares problem $\underset{\alpha\in\mathbb{R}^{s}}{min}\|b-R\alpha\|_2$ - \State Compute minimizer $x^k=S\alpha$ + \For {$k=1,2,3,\ldots$ until convergence (error$<\epsilon_{kryl}$)} \label{algo:conv} + \State $x^k=Solve(A,b,x^{k-1},max\_iter_{kryl})$ \label{algo:solve} + \State retrieve error + \State $S_{k~mod~s}=x^k$ \label{algo:store} + \If {$k$ mod $s=0$ {\bf and} error$>\epsilon_{kryl}$} + \State $R=AS$ \Comment{compute dense matrix} \label{algo:matrix_mul} + \State Solve least-squares problem $\underset{\alpha\in\mathbb{R}^{s}}{min}\|b-R\alpha\|_2$ \label{algo:} + \State $x^k=S\alpha$ \Comment{compute new solution} \EndIf \EndFor \end{algorithmic} \label{algo:01} \end{algorithm} -Operation $S_{k~ mod~ s}=x^k$ consists in copying the residual $x_k$ into the -column $k~ mod~ s$ of the matrix $S$. After the minimization, the matrix $S$ is -reused with the new values of the residuals. +Algorithm~\ref{algo:01} summarizes the principle of our method. The outer +iteration is inside the for loop. Line~\ref{algo:solve}, the Krylov method is +called for a maximum of $max\_iter_{kryl}$ iterations. In practice, we suggest to set this parameter +equals to the restart number of the GMRES-like method. Moreover, a tolerance +threshold must be specified for the solver. In practice, this threshold must be +much smaller than the convergence threshold of the TSARM algorithm (i.e. +$\epsilon$). Line~\ref{algo:store}, $S_{k~ mod~ s}=x^k$ consists in copying the +solution $x_k$ into the column $k~ mod~ s$ of the matrix $S$. After the +minimization, the matrix $S$ is reused with the new values of the residuals. To +solve the minimization problem, an iterative method is used. Two parameters are +required for that: the maximum number of iteration and the threshold to stop the +method. + +To summarize, the important parameters of TSARM are: +\begin{itemize} +\item $\epsilon_{kryl}$ the threshold to stop the method of the krylov method +\item $max\_iter_{kryl}$ the maximum number of iterations for the krylov method +\item $s$ the number of outer iterations before applying the minimization step +\item $max\_iter_{ls}$ the maximum number of iterations for the iterative least-square method +\item $\epsilon_{ls}$ the threshold to stop the least-square method +\end{itemize} %%%********************************************************* %%%********************************************************* @@ -672,11 +686,58 @@ reused with the new values of the residuals. \section{Convergence results} \label{sec:04} + + %%%********************************************************* %%%********************************************************* -\section{Experiments using petsc} +\section{Parallelization} \label{sec:05} +The parallelisation of TSARM relies on the parallelization of all its +parts. More precisely, except the least-square step, all the other parts are +obvious to achieve out in parallel. In order to develop a parallel version of +our code, we have chosen to use PETSc~\cite{petsc-web-page}. For +line~\ref{algo:matrix_mul} the matrix-matrix multiplication is implemented and +efficient since the matrix $A$ is sparse and since the matrix $S$ contains few +colums in practice. As explained previously, at least two methods seem to be +interesting to solve the least-square minimization, CGLS and LSQR. + +In the following we remind the CGLS algorithm. The LSQR method follows more or +less the same principle but it take more place, so we briefly explain the parallelization of CGLS which is similar to LSQR. + +\begin{algorithm}[t] +\caption{CGLS} +\begin{algorithmic}[1] + \Input $A$ (matrix), $b$ (right-hand side) + \Output $x$ (solution vector)\vspace{0.2cm} + \State $r=b-Ax$ + \State $p=A'r$ + \State $s=p$ + \State $g=||s||^2_2$ + \For {$k=1,2,3,\ldots$ until convergence (g$<\epsilon_{ls}$)} \label{algo2:conv} + \State $q=Ap$ + \State $\alpha=g/||q||^2_2$ + \State $x=x+alpha*p$ + \State $r=r-alpha*q$ + \State $s=A'*r$ + \State $g_{old}=g$ + \State $g=||s||^2_2$ + \State $\beta=g/g_{old}$ + \EndFor +\end{algorithmic} +\label{algo:02} +\end{algorithm} + + +In each iteration of CGLS, there is two matrix-vector multiplications and some +classical operations: dots, norm, multiplication and addition on vectors. All +these operations are easy to implement in PETSc or similar environment. + +%%%********************************************************* +%%%********************************************************* +\section{Experiments using petsc} +\label{sec:06} + In order to see the influence of our algorithm with only one processor, we first show a comparison with the standard version of GMRES and our algorithm. In @@ -732,7 +793,7 @@ minimization. \begin{tabular}{|c|c|r|r|r|r|} \hline - \multirow{2}{*}{Matrix name} & Solver / & \multicolumn{2}{c|}{gmres variant} & \multicolumn{2}{c|}{2 stage CGLS} \\ + \multirow{2}{*}{Matrix name} & Solver / & \multicolumn{2}{c|}{GMRES} & \multicolumn{2}{c|}{TSARM CGLS} \\ \cline{3-6} & precond & Time & \# Iter. & Time & \# Iter. \\\hline \hline @@ -753,14 +814,16 @@ torso3 & fgmres / sor & 37.70 & 565 & 34.97 & 510 \\ -Larger experiments .... +Larger experiments ....\\ + +Describe the problems ex15 and ex54 \begin{table*} \begin{center} \begin{tabular}{|r|r|r|r|r|r|r|r|r|} \hline - nb. cores & precond & \multicolumn{2}{c|}{gmres variant} & \multicolumn{2}{c|}{2 stage CGLS} & \multicolumn{2}{c|}{2 stage LSQR} & best gain \\ + nb. cores & precond & \multicolumn{2}{c|}{GMRES} & \multicolumn{2}{c|}{TSARM CGLS} & \multicolumn{2}{c|}{TSARM LSQR} & best gain \\ \cline{3-8} & & Time & \# Iter. & Time & \# Iter. & Time & \# Iter. & \\\hline \hline 2,048 & mg & 403.49 & 18,210 & 73.89 & 3,060 & 77.84 & 3,270 & 5.46 \\ @@ -785,7 +848,7 @@ Larger experiments .... \begin{tabular}{|r|r|r|r|r|r|r|r|r|} \hline - nb. cores & threshold & \multicolumn{2}{c|}{gmres variant} & \multicolumn{2}{c|}{2 stage CGLS} & \multicolumn{2}{c|}{2 stage LSQR} & best gain \\ + nb. cores & threshold & \multicolumn{2}{c|}{GMRES} & \multicolumn{2}{c|}{TSARM CGLS} & \multicolumn{2}{c|}{TSARM LSQR} & best gain \\ \cline{3-8} & & Time & \# Iter. & Time & \# Iter. & Time & \# Iter. & \\\hline \hline 2,048 & 8e-5 & 108.88 & 16,560 & 23.06 & 3,630 & 22.79 & 3,630 & 4.77 \\ @@ -793,7 +856,7 @@ Larger experiments .... 4,096 & 7e-5 & 160.59 & 22,530 & 35.15 & 5,130 & 29.21 & 4,350 & 5.49 \\ 4,096 & 6e-5 & 249.27 & 35,520 & 52.13 & 7,950 & 39.24 & 5,790 & 6.35 \\ 8,192 & 6e-5 & 149.54 & 17,280 & 28.68 & 3,810 & 29.05 & 3,990 & 5.21 \\ - 8,192 & 5e-5 & 792.11 & 109,590 & 76.83 & 10,470 & 65.20 & 9,030 & 12.14 \\ + 8,192 & 5e-5 & 785.04 & 109,590 & 76.07 & 10,470 & 69.42 & 9,030 & 11.30 \\ 16,384 & 4e-5 & 718.61 & 86,400 & 98.98 & 10,830 & 131.86 & 14,790 & 7.26 \\ \hline @@ -802,6 +865,33 @@ Larger experiments .... \label{tab:04} \end{center} \end{table*} + + + + + +\begin{table*} +\begin{center} +\begin{tabular}{|r|r|r|r|r|r|r|r|r|r|r|} +\hline + + nb. cores & \multicolumn{2}{c|}{GMRES} & \multicolumn{2}{c|}{TSARM CGLS} & \multicolumn{2}{c|}{TSARM LSQR} & best gain & \multicolumn{3}{c|}{efficiency} \\ +\cline{2-7} \cline{9-11} + & Time & \# Iter. & Time & \# Iter. & Time & \# Iter. & & GMRES & TS CGLS & TS LSQR\\\hline \hline + 512 & 3,969.69 & 33,120 & 709.57 & 5,790 & 622.76 & 5,070 & 6.37 & 1 & 1 & 1 \\ + 1024 & 1,530.06 & 25,860 & 290.95 & 4,830 & 307.71 & 5,070 & 5.25 & 1.30 & 1.21 & 1.01 \\ + 2048 & 919.62 & 31,470 & 237.52 & 8,040 & 194.22 & 6,510 & 4.73 & 1.08 & .75 & .80\\ + 4096 & 405.60 & 28,380 & 111.67 & 7,590 & 91.72 & 6,510 & 4.42 & 1.22 & .79 & .84 \\ + 8192 & 785.04 & 109,590 & 76.07 & 10,470 & 69.42 & 9,030 & 11.30 & .32 & .58 & .56 \\ + +\hline + +\end{tabular} +\caption{Comparison of FGMRES and 2 stage FGMRES algorithms for ex54 of Petsc (both with the MG preconditioner) with 204,919,225 components on Curie with different number of cores (restart=30, s=12, threshol 5e-5), time is expressed in seconds.} +\label{tab:05} +\end{center} +\end{table*} + %%%********************************************************* %%%********************************************************* @@ -810,7 +900,7 @@ Larger experiments .... %%%********************************************************* %%%********************************************************* \section{Conclusion} -\label{sec:06} +\label{sec:07} %The conclusion goes here. this is more of the conclusion %%%********************************************************* %%%********************************************************* @@ -818,6 +908,7 @@ Larger experiments .... future plan : \\ - study other kinds of matrices, problems, inner solvers\\ +- test the influence of all the parameters\\ - adaptative number of outer iterations to minimize\\ - other methods to minimize the residuals?\\ - implement our solver inside PETSc @@ -852,23 +943,23 @@ Curie and Juqueen respectively based in France and Germany. % http://www.ctan.org/tex-archive/biblio/bibtex/contrib/doc/ % The IEEEtran BibTeX style support page is at: % http://www.michaelshell.org/tex/ieeetran/bibtex/ -%\bibliographystyle{IEEEtran} +\bibliographystyle{IEEEtran} % argument is your BibTeX string definitions and bibliography database(s) -%\bibliography{IEEEabrv,../bib/paper} +\bibliography{biblio} % % manually copy in the resultant .bbl file % set second argument of \begin to the number of references % (used to reserve space for the reference number labels box) -\begin{thebibliography}{1} +%% \begin{thebibliography}{1} -\bibitem{saad86} Y.~Saad and M.~H.~Schultz, \emph{GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems}, SIAM Journal on Scientific and Statistical Computing, 7(3):856--869, 1986. +%% \bibitem{saad86} Y.~Saad and M.~H.~Schultz, \emph{GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems}, SIAM Journal on Scientific and Statistical Computing, 7(3):856--869, 1986. -\bibitem{saad96} Y.~Saad, \emph{Iterative Methods for Sparse Linear Systems}, PWS Publishing, New York, 1996. +%% \bibitem{saad96} Y.~Saad, \emph{Iterative Methods for Sparse Linear Systems}, PWS Publishing, New York, 1996. -\bibitem{hestenes52} M.~R.~Hestenes and E.~Stiefel, \emph{Methods of conjugate gradients for solving linear system}, Journal of Research of National Bureau of Standards, B49:409--436, 1952. +%% \bibitem{hestenes52} M.~R.~Hestenes and E.~Stiefel, \emph{Methods of conjugate gradients for solving linear system}, Journal of Research of National Bureau of Standards, B49:409--436, 1952. -\bibitem{paige82} C.~C.~Paige and A.~M.~Saunders, \emph{LSQR: An Algorithm for Sparse Linear Equations and Sparse Least Squares}, ACM Trans. Math. Softw. 8(1):43--71, 1982. -\end{thebibliography} +%% \bibitem{paige82} C.~C.~Paige and A.~M.~Saunders, \emph{LSQR: An Algorithm for Sparse Linear Equations and Sparse Least Squares}, ACM Trans. Math. Softw. 8(1):43--71, 1982. +%% \end{thebibliography}