accurate performance models. That is why another solution is to use a simulation
tool which allows us to change many parameters of the architecture (network
bandwidth, latency, number of processors) and to simulate the execution of such
-applications. We have decided to use SimGrid as it enables to benchmark MPI
-applications.
+applications. The main contribution of this paper is to show that the use of a
+simulation tool (here we have decided to use the SimGrid toolkit) can really
+help developpers to better tune their applications for a given multi-core
+architecture.
-In this paper, we focus our attention on two parallel iterative algorithms based
+In particular we focus our attention on two parallel iterative algorithms based
on the Multisplitting algorithm and we compare them to the GMRES algorithm.
-These algorithms are used to solve libear systems. Two different variants of
+These algorithms are used to solve linear systems. Two different variants of
the Multisplitting are studied: one using synchronoous iterations and another
-one with asynchronous iterations. For each algorithm we have tested different
-parameters to see their influence. We strongly recommend people interested
-by investing into a new expensive hardware architecture to benchmark
-their applications using a simulation tool before.
-
-
-
+one with asynchronous iterations. For each algorithm we have simulated
+different architecture parameters to evaluate their influence on the overall
+execution time. The obtain simulated results confirm the real results
+previously obtained on different real multi-core architectures and also confirm
+the efficiency of the asynchronous multisplitting algorithm compared to the
+synchronous GMRES method.
\end{abstract}
\label{sec:04}
\subsection{Synchronous and asynchronous two-stage methods for sparse linear systems}
\label{sec:04.01}
-In this paper we focus on two-stage multisplitting methods in their both versions (synchronous and asynchronous)~\cite{Frommer92,Szyld92,Bru95}. These iterative methods are based on multisplitting methods~\cite{O'leary85,White86,Alefeld97} and use two nested iterations: the outer iteration and the inner iteration. Let us consider the following sparse linear system of $n$ equations in $\mathbb{R}$
+In this paper we focus on two-stage multisplitting methods in their both versions (synchronous and asynchronous)~\cite{Frommer92,Szyld92,Bru95}. These iterative methods are based on multisplitting methods~\cite{O'leary85,White86,Alefeld97} and use two nested iterations: the outer iteration and the inner iteration. Let us consider the following sparse linear system of $n$ equations in $\mathbb{R}$:
\begin{equation}
Ax=b,
\label{eq:01}
\end{equation}
-where $A$ is a sparse square and nonsingular matrix, $b$ is the right-hand side and $x$ is the solution of the system. Our work in this paper is restricted to the block Jacobi splitting method. This approach of multisplitting consists in partitioning the matrix $A$ into $L$ horizontal band matrices of order $\frac{n}{L}\times n$ without overlapping (i.e. sub-vectors $\{x_\ell\}_{1\leq\ell\leq L}$ are disjoint). Two-stage multisplitting methods solve the linear system~(\ref{eq:01}) iteratively as follows
+where $A$ is a sparse square and nonsingular matrix, $b$ is the right-hand side and $x$ is the solution of the system. Our work in this paper is restricted to the block Jacobi splitting method. This approach of multisplitting consists in partitioning the matrix $A$ into $L$ horizontal band matrices of order $\frac{n}{L}\times n$ without overlapping (i.e. sub-vectors $\{x_\ell\}_{1\leq\ell\leq L}$ are disjoint). Two-stage multisplitting methods solve the linear system~(\ref{eq:01}) iteratively as follows:
\begin{equation}
x_\ell^{k+1} = A_{\ell\ell}^{-1}(b_\ell - \displaystyle\sum^{L}_{\substack{m=1\\m\neq\ell}}{A_{\ell m}x^k_m}),\mbox{~for~}\ell=1,\ldots,L\mbox{~and~}k=1,2,3,\ldots
\label{eq:02}
\end{equation}
-where $x_\ell$ are sub-vectors of the solution $x$, $b_\ell$ are the sub-vectors of the right-hand side $b$, and $A_{\ell\ell}$ and $A_{\ell m}$ are diagonal and off-diagonal blocks of matrix $A$ respectively. The iterations of these methods can naturally be computed in parallel such that each processor or cluster of processors is responsible for solving one splitting as a linear sub-system
+where $x_\ell$ are sub-vectors of the solution $x$, $b_\ell$ are the sub-vectors of the right-hand side $b$, and $A_{\ell\ell}$ and $A_{\ell m}$ are diagonal and off-diagonal blocks of matrix $A$ respectively. The iterations of these methods can naturally be computed in parallel such that each processor or cluster of processors is responsible for solving one splitting as a linear sub-system:
\begin{equation}
A_{\ell\ell} x_\ell = c_\ell,\mbox{~for~}\ell=1,\ldots,L,
\label{eq:03}
\end{equation}
-where right-hand sides $c_\ell=b_\ell-\sum_{m\neq\ell}A_{\ell m}x_m$ are computed using the shared vectors $x_m$. In this paper, we use the well-known iterative method GMRES ({\it Generalized Minimal RESidual})~\cite{saad86} as an inner iteration to approximate the solutions of the different splittings arising from the block Jacobi multisplitting of matrix $A$. The algorithm in Figure~\ref{alg:01} shows the main key points of our block Jacobi two-stage method executed by a cluster of processors. In line~\ref{solve}, the linear sub-system~(\ref{eq:03}) is solved in parallel using GMRES method where $\MIG$ and $\TOLG$ are the maximum number of inner iterations and the tolerance threshold for GMRES respectively. The convergence of the two-stage multisplitting methods, based on synchronous or asynchronous iterations, is studied by many authors for example~\cite{Bru95,bahi07}.
+where right-hand sides $c_\ell=b_\ell-\sum_{m\neq\ell}A_{\ell m}x_m$ are computed using the shared vectors $x_m$. In this paper, we use the well-known iterative method GMRES ({\it Generalized Minimal RESidual})~\cite{saad86} as an inner iteration to approximate the solutions of the different splittings arising from the block Jacobi multisplitting of matrix $A$. The algorithm in Figure~\ref{alg:01} shows the main key points of our block Jacobi two-stage method executed by a cluster of processors. In line~\ref{solve}, the linear sub-system~(\ref{eq:03}) is solved in parallel using GMRES method where $\MIG$ and $\TOLG$ are the maximum number of inner iterations and the tolerance threshold for GMRES respectively. The convergence of the two-stage multisplitting methods, based on synchronous or asynchronous iterations, has been studied by many authors for example~\cite{Bru95,bahi07}.
\begin{figure}[t]
%\begin{algorithm}[t]
%\end{algorithm}
\end{figure}
-In this paper, we propose two algorithms of two-stage multisplitting methods. The first algorithm is based on the asynchronous model which allows the communications to be overlapped by computations and reduces the idle times resulting from the synchronizations. So in the asynchronous mode, our two-stage algorithm uses asynchronous outer iterations and asynchronous communications between clusters. The communications (i.e. lines~\ref{send} and~\ref{recv} in Figure~\ref{alg:01}) are performed by message passing using MPI non-blocking communication routines. The convergence of the asynchronous iterations is detected when all clusters have locally converged
+In this paper, we propose two algorithms of two-stage multisplitting methods. The first algorithm is based on the asynchronous model which allows communications to be overlapped by computations and reduces the idle times resulting from the synchronizations. So in the asynchronous mode, our two-stage algorithm uses asynchronous outer iterations and asynchronous communications between clusters. The communications (i.e. lines~\ref{send} and~\ref{recv} in Figure~\ref{alg:01}) are performed by message passing using MPI non-blocking communication routines. The convergence of the asynchronous iterations is detected when all clusters have locally converged:
\begin{equation}
k\geq\MIM\mbox{~or~}\|x_\ell^{k+1}-x_\ell^k\|_{\infty }\leq\TOLM,
\label{eq:04}
\end{equation}
where $\MIM$ is the maximum number of outer iterations and $\TOLM$ is the tolerance threshold for the two-stage algorithm.
-The second two-stage algorithm is based on synchronous outer iterations. We propose to use the Krylov iteration based on residual minimization to improve the slow convergence of the multisplitting methods. In this case, a $n\times s$ matrix $S$ is set using solutions issued from the inner iteration
+The second two-stage algorithm is based on synchronous outer iterations. We propose to use the Krylov iteration based on residual minimization to improve the slow convergence of the multisplitting methods. In this case, a $n\times s$ matrix $S$ is set using solutions issued from the inner iteration:
\begin{equation}
S=[x^1,x^2,\ldots,x^s],~s\ll n.
\label{eq:05}
\end{equation}
-At each $s$ outer iterations, the algorithm computes a new approximation $\tilde{x}=S\alpha$ which minimizes the residual
+At each $s$ outer iterations, the algorithm computes a new approximation $\tilde{x}=S\alpha$ which minimizes the residual:
\begin{equation}
\min_{\alpha\in\mathbb{R}^s}{\|b-AS\alpha\|_2}.
\label{eq:06}
%\end{algorithm}
\end{figure}
-\subsection{Simulation of two-stage methods using SimGrid framework}
+\subsection{Simulation of the two-stage methods using SimGrid toolkit}
\label{sec:04.02}
One of our objectives when simulating the application in Simgrid is, as in real
-life, to get accurate results (solutions of the problem) but also ensure the
+life, to get accurate results (solutions of the problem) but also to ensure the
test reproducibility under the same conditions. According to our experience,
very few modifications are required to adapt a MPI program for the Simgrid
simulator using SMPI (Simulator MPI). The first modification is to include SMPI
suppress all global variables by replacing them with local variables or using a
Simgrid selector called "runtime automatic switching"
(smpi/privatize\_global\_variables). Indeed, global variables can generate side
-effects on runtime between the threads running in the same process, generated by
+effects on runtime between the threads running in the same process and generated by
Simgrid to simulate the grid environment.
%\RC{On vire cette phrase ?} \RCE {Si c'est la phrase d'avant sur les threads, je pense qu'on peut la retenir car c'est l'explication du pourquoi Simgrid n'aime pas les variables globales. Si c'est pas bien dit, on peut la reformuler. Si c'est la phrase ci-apres, effectivement, on peut la virer si elle preterais a discussion}The
\begin{itemize}
\item maximum number of inner and outer iterations;
\item inner and outer precisions;
- \item maximum number of the gmres's restarts in the Arnorldi process;
- \item maximum number of iterations qnd the tolerance threshold in classical GMRES;
+ \item maximum number of the GMRES restarts in the Arnorldi process;
+ \item maximum number of iterations and the tolerance threshold in classical GMRES;
\item tolerance threshold for outer and inner-iterations;
- \item matrix size (N$_{x}$, N$_{y}$ and N$_{z}$) respectively on x, y, z axis;
- \item matrix diagonal value = 6.0 for synchronous Krylov multisplitting experiments and 6.2 for asynchronous block Jacobi experiments; \RC{CE tu vérifies, je dis ca de tête}
+ \item matrix size (N$_{x}$, N$_{y}$ and N$_{z}$) respectively on $x, y, z$ axis;
+ \item matrix diagonal value is fixed to $6.0$ for synchronous Krylov multisplitting experiments and $6.2$ for asynchronous block Jacobi experiments; \RC{CE tu vérifies, je dis ca de tête}
\item matrix off-diagonal value;
\item execution mode: synchronous or asynchronous;
\RCE {C'est ok la liste des arguments du programme mais si Lilia ou toi pouvez preciser pour les arguments pour CGLS ci dessous} \RC{Vu que tu n'as pas fait varier ce paramètre, on peut ne pas en parler}
\item Maximum number of iterations and tolerance threshold for CGLS.
\end{itemize}
-It should also be noticed that both solvers have been executed with the Simgrid selector -cfg=smpi/running\_power which determines the computational power (here 19GFlops) of the simulator host machine.
+It should also be noticed that both solvers have been executed with the Simgrid selector \texttt{-cfg=smpi/running\_power} which determines the computational power (here 19GFlops) of the simulator host machine.
%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%
In this section, experiments for both Multisplitting algorithms are reported. First the 3D Poisson problem used in our experiments is described.
-\subsection{3D Poisson}
+\subsection{The 3D Poisson problem}
-We use our two-stage algorithms to solve the well-known Poisson problem $\nabla^2\phi=f$~\cite{Polyanin01}. In three-dimensional Cartesian coordinates in $\mathbb{R}^3$, the problem takes the following form
+We use our two-stage algorithms to solve the well-known Poisson problem $\nabla^2\phi=f$~\cite{Polyanin01}. In three-dimensional Cartesian coordinates in $\mathbb{R}^3$, the problem takes the following form:
\begin{equation}
\frac{\partial^2}{\partial x^2}\phi(x,y,z)+\frac{\partial^2}{\partial y^2}\phi(x,y,z)+\frac{\partial^2}{\partial z^2}\phi(x,y,z)=f(x,y,z)\mbox{~in the domain~}\Omega
\label{eq:07}
\end{equation}
-such that
+such that:
\begin{equation*}
\phi(x,y,z)=0\mbox{~on the boundary~}\partial\Omega
\end{equation*}
-where the real-valued function $\phi(x,y,z)$ is the solution sought, $f(x,y,z)$ is a known function and $\Omega=[0,1]^3$. The 3D discretization of the Laplace operator $\nabla^2$ with the finite difference scheme includes 7 points stencil on the computational grid. The numerical approximation of the Poisson problem on three-dimensional grid is repeatedly computed as $\phi=\phi^\star$ such that
+where the real-valued function $\phi(x,y,z)$ is the solution sought, $f(x,y,z)$ is a known function and $\Omega=[0,1]^3$. The 3D discretization of the Laplace operator $\nabla^2$ with the finite difference scheme includes 7 points stencil on the computational grid. The numerical approximation of the Poisson problem on three-dimensional grid is repeatedly computed as $\phi=\phi^\star$ such that:
\begin{equation}
\begin{array}{ll}
\phi^\star(x,y,z)=&\frac{1}{6}(\phi(x-h,y,z)+\phi(x,y-h,z)+\phi(x,y,z-h)\\&+\phi(x+h,y,z)+\phi(x,y+h,z)+\phi(x,y,z+h)\\&-h^2f(x,y,z))
In the parallel context, the 3D Poisson problem is partitioned into $L\times p$ sub-problems such that $L$ is the number of clusters and $p$ is the number of processors in each cluster. We apply the three-dimensional partitioning instead of the row-by-row one in order to reduce the size of the data shared at the sub-problems boundaries. In this case, each processor is in charge of parallelepipedic block of the problem and has at most six neighbors in the same cluster or in distant clusters with which it shares data at boundaries.
-\subsection{Study setup and Simulation Methodology}
+\subsection{Study setup and simulation methodology}
First, to conduct our study, we propose the following methodology
which can be reused for any grid-enabled applications.\\
the application to be tested. Numerical parallel iterative algorithms
have been chosen for the study in this paper. \\
-\textbf{Step 2}: Collect the software materials needed for the
-experimentation. In our case, we have two variants algorithms for the
-resolution of the 3D-Poisson problem: (1) using the classical GMRES; (2) and the Multisplitting method. In addition, the Simgrid simulator has been chosen to simulate the behaviors of the
-distributed applications. Simgrid is running on the Mesocentre datacenter in the University of Franche-Comte and also in a virtual machine on a simple laptop. \\
+\textbf{Step 2}: Collect the software materials needed for the experimentation.
+In our case, we have two variants algorithms for the resolution of the
+3D-Poisson problem: (1) using the classical GMRES; (2) and the Multisplitting
+method. In addition, the Simgrid simulator has been chosen to simulate the
+behaviors of the distributed applications. Simgrid is running in a virtual
+machine on a simple laptop. \\
\textbf{Step 3}: Fix the criteria which will be used for the future
results comparison and analysis. In the scope of this study, we retain
capacity" of the network is defined as the maximum of data that can transit
from one point to another in a unit of time.
\item the network latency (lat : microsecond) defined as the delay from the
- start time to send the data from a source and the final time the destination
- have finished to receive it.
+ start time to send a simple data from a source to a destination.
\end{enumerate}
-Upon the network characteristics, another impacting factor is the
-application dependent volume of data exchanged between the nodes in the cluster
-and between distant clusters. Large volume of data can be transferred and
-transit between the clusters and nodes during the code execution.
+Upon the network characteristics, another impacting factor is the volume of data exchanged between the nodes in the cluster
+and between distant clusters. This parameter is application dependent.
In a grid environment, it is common to distinguish, on the one hand, the
- "intra-network" which refers to the links between nodes within a cluster and,
+ "intra-network" which refers to the links between nodes within a cluster and
on the other hand, the "inter-network" which is the backbone link between
- clusters. In practice, these two networks have different speeds. The
- intra-network generally works like a high speed local network with a high
- bandwith and very low latency. In opposite, the inter-network connects clusters
- sometime via heterogeneous networks components throuth internet with a lower
- speed. The network between distant clusters might be a bottleneck for the
- global performance of the application.
+ clusters. In practice, these two networks have different speeds.
+ The intra-network generally works like a high speed local network with a
+ high bandwith and very low latency. In opposite, the inter-network connects
+ clusters sometime via heterogeneous networks components throuth internet with
+ a lower speed. The network between distant clusters might be a bottleneck
+ for the global performance of the application.
\subsection{Comparison of GMRES and Krylov Multisplitting algorithms in synchronous mode}
\subsection{Comparing GMRES in native synchronous mode and the multisplitting algorithm in asynchronous mode}
The previous paragraphs put in evidence the interests to simulate the behavior
-of the application before any deployment in a real environment. We have focused
-the study on analyzing the performance in varying the key factors impacting the
-results. The study compares the performance of the two proposed algorithms both
-in \textit{synchronous mode }. In this section, following the same previous
-methodology, the goal is to demonstrate the efficiency of the multisplitting
-method in \textit{ asynchronous mode} compared with the classical GMRES staying
-in \textit{synchronous mode}.
-
-Note that the interest of using the asynchronous mode for data exchange
-is mainly, in opposite of the synchronous mode, the non-wait aspects of
-the current computation after a communication operation like sending
-some data between nodes. Each processor can continue their local
-calculation without waiting for the end of the communication. Thus, the
-asynchronous may theoretically reduce the overall execution time and can
-improve the algorithm performance.
-
-As stated supra, Simgrid simulator tool has been used to prove the
-efficiency of the multisplitting in asynchronous mode and to find the
-best combination of the grid resources (CPU, Network, input matrix size,
-\ldots ) to get the highest \textit{"relative gain"} (exec\_time$_{GMRES}$ / exec\_time$_{multisplitting}$) in comparison with the classical GMRES time.
+of the application before any deployment in a real environment. In this
+section, following the same previous methodology, our goal is to compare the
+efficiency of the multisplitting method in \textit{ asynchronous mode} with the
+classical GMRES in \textit{synchronous mode}.
+
+The interest of using an asynchronous algorithm is that there is no more
+synchronization. With geographically distant clusters, this may be essential.
+In this case, each processor can compute its iteration freely without any
+synchronization with the other processors. Thus, the asynchronous may
+theoretically reduce the overall execution time and can improve the algorithm
+performance.
+
+\RC{la phrase suivante est bizarre, je ne comprends pas pourquoi elle vient ici}
+As stated before, the Simgrid simulator tool has been successfully used to show
+the efficiency of the multisplitting in asynchronous mode and to find the best
+combination of the grid resources (CPU, Network, input matrix size, \ldots ) to
+get the highest \textit{"relative gain"} (exec\_time$_{GMRES}$ /
+exec\_time$_{multisplitting}$) in comparison with the classical GMRES time.
The test conditions are summarized in the table below : \\
-% environment
-\begin{footnotesize}
+\begin{figure} [ht!]
+\centering
\begin{tabular}{r c }
\hline
Grid & 2x50 totaling 100 processors\\ %\hline
Input matrix size & N$_{x}$ = From 62 to 150\\ %\hline
Residual error precision & 10$^{-5}$ to 10$^{-9}$\\ \hline \\
\end{tabular}
-\end{footnotesize}
+\end{figure}
-Again, comprehensive and extensive tests have been conducted varying the
-CPU power and the network parameters (bandwidth and latency) in the
-simulator tool with different problem size. The relative gains greater
-than 1 between the two algorithms have been captured after each step of
-the test. Table 7 below has recorded the best grid configurations
-allowing the multisplitting method execution time more performant 2.5 times than
-the classical GMRES execution and convergence time. The experimentation has demonstrated the relative multisplitting algorithm tolerance when using a low speed network that we encounter usually with distant clusters thru the internet.
+Again, comprehensive and extensive tests have been conducted with different
+parametes as the CPU power, the network parameters (bandwidth and latency) in
+the simulator tool and with different problem size. The relative gains greater
+than 1 between the two algorithms have been captured after each step of the
+test. In Figure~\ref{table:01} are reported the best grid configurations
+allowing the multisplitting method to be more than 2.5 times faster than the
+classical GMRES. These experiments also show the relative tolerance of the
+multisplitting algorithm when using a low speed network as usually observed with
+geographically distant clusters throuth the internet.
% use the same column width for the following three tables
\newlength{\mytablew}\settowidth{\mytablew}{\footnotesize\np{E-11}}
\end{tabular}}
-\begin{table}[!t]
- \centering
+\begin{figure}[!t]
+\centering
+%\begin{table}
% \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}
% \label{"Table 7"}
-Table 7. Relative gain of the multisplitting algorithm compared with
-the classical GMRES \\
-
- \begin{mytable}{11}
+ \begin{mytable}{11}
\hline
bandwidth (Mbit/s)
& 5 & 5 & 5 & 5 & 5 & 50 & 50 & 50 & 50 & 50 \\
& 2.52 & 2.55 & 2.52 & 2.57 & 2.54 & 2.53 & 2.51 & 2.58 & 2.55 & 2.54 \\
\hline
\end{mytable}
-\end{table}
+%\end{table}
+ \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}
+ \label{table:01}
+\end{figure}
+
\section{Conclusion}
CONCLUSION
