X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/hpcc2014.git/blobdiff_plain/8e535991311d246854e7597c06cdee25b67c8419..f9bb0366521948860427dbe75c159008da521ac3:/hpcc.tex

diff --git a/hpcc.tex b/hpcc.tex
index c9606c3..e1d916e 100644
--- a/hpcc.tex
+++ b/hpcc.tex
@@ -31,6 +31,8 @@
   \todo[color=blue!10,#1]{\sffamily\textbf{LZK:} #2}\xspace}
 \newcommand{\RC}[2][inline]{%
   \todo[color=red!10,#1]{\sffamily\textbf{RC:} #2}\xspace}
+\newcommand{\CER}[2][inline]{%
+  \todo[color=pink!10,#1]{\sffamily\textbf{CER:} #2}\xspace}
 
 \algnewcommand\algorithmicinput{\textbf{Input:}}
 \algnewcommand\Input{\item[\algorithmicinput]}
@@ -149,8 +151,8 @@ approach of the simulation of AIAC algorithms using a simulation tool (i.e. the
 SimGrid toolkit~\cite{SimGrid}). Second, we confirm the effectiveness of
 asynchronous mode algorithms by comparing their performance with the synchronous
 mode. More precisely, we had implemented a program for solving large
-non-symmetric linear system of equations by numerical method GMRES (Generalized
-Minimal Residual) []\AG[]{[]?}. We show, that with minor modifications of the
+linear system of equations by numerical method GMRES (Generalized
+Minimal Residual) \cite{ref1}. We show, that with minor modifications of the
 initial MPI code, the SimGrid toolkit allows us to perform a test campaign of a
 real AIAC application on different computing architectures. The simulated
 results we obtained are in line with real results exposed in ??\AG[]{??}.
@@ -235,21 +237,23 @@ SimGrid provides several programming interfaces: MSG to simulate Concurrent
 Sequential Processes, SimDAG to simulate DAGs of (parallel) tasks, and SMPI to
 run real applications written in MPI~\cite{MPI}.  Apart from the native C
 interface, SimGrid provides bindings for the C++, Java, Lua and Ruby programming
-languages.  The SMPI interface supports applications written in C or Fortran,
-with little or no modifications.  SMPI implements about \np[\%]{80} of the MPI
-2.0 standard~\cite{bedaride:hal-00919507}.
-
-%%% explain simulation
-%- simulated processes folded in one real process
-%- simulates interactions on the network, fluid model
-%- able to skip long-lasting computations
-%- traces + visu?
-
-%%% platforms
-%- describe resources and their interconnection, with their properties
-%- XML files
-
-%%% validation + refs
+languages.  SMPI is the interface that has been used for the work exposed in
+this paper.  The SMPI interface implements about \np[\%]{80} of the MPI 2.0
+standard~\cite{bedaride:hal-00919507}, and supports applications written in C or
+Fortran, with little or no modifications.
+
+With SimGrid, the execution of a distributed application is simulated on a
+single machine.  The application code is really executed, but some operations
+like the communications are intercepted to be simulated according to the
+characteristics of the simulated execution platform.  The description of this
+target platform is given as an input for the execution, by the mean of an XML
+file.  It describes the properties of the platform, such as the computing node
+with their computing power, the interconnection links with their bandwidth and
+latency, and the routing strategy.  The simulated running time of the
+application is computed according to these properties.
+
+\AG{Faut-il ajouter quelque-chose ?} 
+\CER{Comme tu as dÃ©crit la plateforme d'exÃ©cution, on peut ajouter Ã©ventuellement le fichier XML contenant des hosts dans les clusters formant la grille} 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Simulation of the multisplitting method}
@@ -318,19 +322,7 @@ is solved independently by a cluster and communications are required to update t
 \label{algo:01}
 \end{figure}
 
-Algorithm on Figure~\ref{algo:01} shows the main key points of the
-multisplitting method to solve a large sparse linear system. This algorithm is
-based on an outer-inner iteration method where the parallel synchronous GMRES
-method is used to solve the inner iteration. It is executed in parallel by each
-cluster of processors. For all $l,m\in\{1,\ldots,L\}$, the matrices and vectors
-with the subscript $l$ represent the local data for cluster $l$, while
-$\{A_{lm}\}_{m\neq l}$ are off-diagonal matrices of sparse matrix $A$ and
-$\{X_m\}_{m\neq l}$ contain vector elements of solution $x$ shared with
-neighboring clusters. At every outer iteration $k$, asynchronous communications
-are performed between processors of the local cluster and those of distant
-clusters (lines~\ref{algo:01:send} and~\ref{algo:01:recv} in
-Figure~\ref{algo:01}). The shared vector elements of the solution $x$ are
-exchanged by message passing using MPI non-blocking communication routines.
+Algorithm on Figure~\ref{algo:01} shows the main key points of the multisplitting method to solve a large sparse linear system. This algorithm is based on an outer-inner iteration method where the parallel synchronous GMRES method is used to solve the inner iteration. It is executed in parallel by each cluster of processors. For all $l,m\in\{1,\ldots,L\}$, the matrices and vectors with the subscript $l$ represent the local data for cluster $l$, while $\{A_{lm}\}_{m\neq l}$ are off-diagonal matrices of sparse matrix $A$ and $\{X_m\}_{m\neq l}$ contain vector elements of solution $x$ shared with neighboring clusters. At every outer iteration $k$, asynchronous communications are performed between processors of the local cluster and those of distant clusters (lines~\ref{algo:01:send} and~\ref{algo:01:recv} in Figure~\ref{algo:01}). The shared vector elements of the solution $x$ are exchanged by message passing using MPI non-blocking communication routines.
 
 \begin{figure}[!t]
 \centering
@@ -339,61 +331,32 @@ exchanged by message passing using MPI non-blocking communication routines.
 \label{fig:4.1}
 \end{figure}
 
-The global convergence of the asynchronous multisplitting solver is detected
-when the clusters of processors have all converged locally. We implemented the
-global convergence detection process as follows. On each cluster a master
-processor is designated (for example the processor with rank 1) and masters of
-all clusters are interconnected by a virtual unidirectional ring network (see
-Figure~\ref{fig:4.1}). During the resolution, a Boolean token circulates around
-the virtual ring from a master processor to another until the global convergence
-is achieved. So starting from the cluster with rank 1, each master processor $i$
-sets the token to \textit{True} if the local convergence is achieved or to
-\text\it{False} otherwise, and sends it to master processor $i+1$. Finally, the
-global convergence is detected when the master of cluster 1 receives from the
-master of cluster $L$ a token set to \textit{True}. In this case, the master of
-cluster 1 broadcasts a stop message to masters of other clusters. In this work,
-the local convergence on each cluster $l$ is detected when the following
-condition is satisfied
+The global convergence of the asynchronous multisplitting solver is detected when the clusters of processors have all converged locally. We implemented the global convergence detection process as follows. On each cluster a master processor is designated (for example the processor with rank 1) and masters of all clusters are interconnected by a virtual unidirectional ring network (see Figure~\ref{fig:4.1}). During the resolution, a Boolean token circulates around the virtual ring from a master processor to another until the global convergence is achieved. So starting from the cluster with rank 1, each master processor $i$ sets the token to {\it True} if the local convergence is achieved or to {\it False} otherwise, and sends it to master processor $i+1$. Finally, the global convergence is detected when the master of cluster 1 receives from the master of cluster $L$ a token set to {\it True}. In this case, the master of cluster 1 broadcasts a stop message to masters of other clusters. In this work, the local convergence on each cluster $l$ is detected when the following condition is satisfied
 \begin{equation*}
   (k\leq \MI) \text{ or } (\|X_l^k - X_l^{k+1}\|_{\infty}\leq\epsilon)
 \end{equation*}
 where $\MI$ is the maximum number of outer iterations and $\epsilon$ is the tolerance threshold of the error computed between two successive local solution $X_l^k$ and $X_l^{k+1}$. 
 
-\LZK{Description du processus d'adaptation de l'algo multisplitting Ã  SimGrid}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-We did not encounter major blocking problems when adapting the multisplitting
-algorithm previously described to a simulation environment like SimGrid unless
-some code debugging. Indeed, apart from the review of the program sequence for
-asynchronous exchanges between the six neighbors of each point in a submatrix
-within a cluster or between clusters, the algorithm was executed successfully
-with SMPI and provided identical outputs as those obtained with direct execution
-under MPI. In synchronous mode, the execution of the program raised no
-particular issue but in asynchronous mode, the review of the sequence of
-MPI\_Isend, MPI\_Irecv and MPI\_Waitall instructions and with the addition of
-the primitive MPI\_Test was needed to avoid a memory fault due to an infinite
-loop resulting from the non-convergence of the algorithm. Note here that the use
-of SMPI functions optimizer for memory footprint and CPU usage is not
-recommended knowing that one wants to get real results by simulation.  As
-mentioned, upon this adaptation, the algorithm is executed as in the real life
-in the simulated environment after the following minor changes. First, all
-declared global variables have been moved to local variables for each
-subroutine. In fact, global variables generate side effects arising from the
-concurrent access of shared memory used by threads simulating each computing
-units in the SimGrid architecture. Second, the alignment of certain types of
-variables such as ``long int'' had also to be reviewed. Finally, some
-compilation errors on MPI\_Waitall and MPI\_Finalize primitives have been fixed
-with the latest version of SimGrid.  In total, the initial MPI program running
-on the simulation environment SMPI gave after a very simple adaptation the same
-results as those obtained in a real environment. We have tested in synchronous
-mode with a simulated platform starting from a modest 2 or 3 clusters grid to a
-larger configuration like simulating Grid5000 with more than 1500 hosts with
-5000 cores~\cite{bolze2006grid}. Once the code debugging and adaptation were
-complete, the next section shows our methodology and experimental results.
+We did not encounter major blocking problems when adapting the multisplitting algorithm previously described to a simulation environment like SimGrid unless some code 
+debugging. Indeed, apart from the review of the program sequence for asynchronous exchanges between processors within a cluster or between clusters, the algorithm was executed successfully with SMPI and provided identical outputs as those obtained with direct execution under MPI. In synchronous 
+mode, the execution of the program raised no particular issue but in asynchronous mode, the review of the sequence of MPI\_Isend, MPI\_Irecv and MPI\_Waitall instructions
+and with the addition of the primitive MPI\_Test was needed to avoid a memory fault due to an infinite loop resulting from the non-convergence of the algorithm.
+\CER{On voulait en fait montrer la simplicitÃ© de l'adaptation de l'algo a SimGrid. Les problÃ¨mes rencontrÃ©s dÃ©crits dans ce paragraphe concerne surtout le mode async}\LZK{OK. J'aurais prÃ©fÃ©rÃ© avoir un peu plus de dÃ©tails sur l'adaptation de la version async}
+Note here that the use of SMPI functions optimizer for memory footprint and CPU usage is not recommended knowing that one wants to get real results by simulation.
+As mentioned, upon this adaptation, the algorithm is executed as in the real life in the simulated environment after the following minor changes. First, all declared 
+global variables have been moved to local variables for each subroutine. In fact, global variables generate side effects arising from the concurrent access of 
+shared memory used by threads simulating each computing unit in the SimGrid architecture. Second, the alignment of certain types of variables such as ``long int'' had
+also to be reviewed. Finally, some compilation errors on MPI\_Waitall and MPI\_Finalize primitives have been fixed with the latest version of SimGrid.
+In total, the initial MPI program running on the simulation environment SMPI gave after a very simple adaptation the same results as those obtained in a real 
+environment. We have tested in synchronous mode with a simulated platform starting from a modest 2 or 3 clusters grid to a larger configuration like simulating 
+Grid5000 with more than 1500 hosts with 5000 cores~\cite{bolze2006grid}.
+
 
 
 \section{Experimental results}
 
-When the \emph{real} application runs in the simulation environment and produces the expected results, varying the input
+When the \textit{real} application runs in the simulation environment and produces the expected results, varying the input
 parameters and the program arguments allows us to compare outputs from the code execution. We have noticed from this
 study that the results depend on the following parameters:  
 \begin{itemize}
@@ -402,21 +365,54 @@ study that the results depend on the following parameters:
 \item Hosts power (GFlops) can also influence on the results.
 \item Finally, when submitting job batches for execution, the arguments values
   passed to the program like the maximum number of iterations or the
-  \emph{external} precision are critical. They allow to ensure not only the
+  \textit{external} precision are critical. They allow to ensure not only the
   convergence of the algorithm but also to get the main objective of the
   experimentation of the simulation in having an execution time in asynchronous
   less than in synchronous mode (i.e. speed-up less than 1).
 \end{itemize}
+\LZK{Propositions pour remplacer le terme ``speedup'': acceleration ratio ou relative gain}
 
 A priori, obtaining a speedup less than 1 would be difficult in a local area
 network configuration where the synchronous mode will take advantage on the
 rapid exchange of information on such high-speed links. Thus, the methodology
 adopted was to launch the application on clustered network. In this last
 configuration, degrading the inter-cluster network performance will
-\emph{penalize} the synchronous mode allowing to get a speedup lower than 1.
+\textit{penalize} the synchronous mode allowing to get a speedup lower than 1.
 This action simulates the case of clusters linked with long distance network
 like Internet.
 
+In this paper, we solve the 3D Poisson problem whose the mathematical model is 
+\begin{equation}
+\left\{
+\begin{array}{l}
+\nabla^2 u = f \text{~in~} \Omega \\
+u =0 \text{~on~} \Gamma =\partial\Omega
+\end{array}
+\right.
+\label{eq:02}
+\end{equation}
+where $\nabla^2$ is the Laplace operator, $f$ and $u$ are real-valued functions, and $\Omega=[0,1]^3$. The spatial discretization with a finite difference scheme reduces problem~(\ref{eq:02}) to a system of sparse linear equations. The general iteration scheme of our multisplitting method in a 3D domain using a seven point stencil could be written as 
+\begin{equation}
+\begin{array}{ll}
+u^{k+1}(x,y,z)= & u^k(x,y,z) - \frac{1}{6}\times\\
+               & (u^k(x-1,y,z) + u^k(x+1,y,z) + \\
+               & u^k(x,y-1,z) + u^k(x,y+1,z) + \\
+               & u^k(x,y,z-1) + u^k(x,y,z+1)),
+\end{array}
+\label{eq:03}
+\end{equation} 
+where the iteration matrix $A$ of size $N_x\times N_y\times N_z$ of the discretized linear system is sparse, symmetric and positive definite. 
+
+The parallel solving of the 3D Poisson problem with our multisplitting method requires a data partitioning of the problem between clusters and between processors within a cluster. We have chosen the 3D partitioning instead of the row-by-row partitioning in order to reduce the data exchanges at sub-domain boundaries. Figure~\ref{fig:4.2} shows an example of the data partitioning of the 3D Poisson problem between two clusters of processors, where each sub-problem is assigned to a processor. In this context, a processor has at most six neighbors within a cluster or in distant clusters with which it shares data at sub-domain boundaries. 
+
+\begin{figure}[!t]
+\centering
+  \includegraphics[width=80mm,keepaspectratio]{partition}
+\caption{Example of the 3D data partitioning between two clusters of processors.}
+\label{fig:4.2}
+\end{figure}
+
+
 As a first step, the algorithm was run on a network consisting of two clusters
 containing 50 hosts each, totaling 100 hosts. Various combinations of the above
 factors have providing the results shown in Table~\ref{tab.cluster.2x50} with a
@@ -563,7 +559,11 @@ lat latency, \dots{}).
 	\item Maximum number of internal and external iterations;
 	\item Internal and external precisions;
 	\item Matrix size $N_x$, $N_y$ and $N_z$;
+%<<<<<<< HEAD
 	\item Matrix diagonal value: \np{6.0};
+	\item Matrix Off-diagonal value: \np{-1.0};
+%=======
+%>>>>>>> 5fb6769d88c1720b6480a28521119ef010462fa6
 	\item Execution Mode: synchronous or asynchronous.
 \end{itemize}
 
@@ -603,6 +603,8 @@ with 200 nodes in total. The convergence with a speedup of \np[\%]{90} was
 obtained with a bandwidth of \np[Mbit/s]{1} as shown in
 Table~\ref{tab.cluster.3x67}.
 
+\LZK{Dans le papier, on compare les deux versions synchrone et asycnhrone du multisplitting. Y a t il des rÃ©sultats pour comparer gmres parallÃ¨le classique avec multisplitting asynchrone? Ca permettra de montrer l'intÃ©rÃªt du multisplitting asynchrone sur des clusters distants}
+
 \section{Conclusion}
 The experimental results on executing a parallel iterative algorithm in 
 asynchronous mode on an environment simulating a large scale of virtual 
@@ -631,12 +633,13 @@ demonstrated an original solution to optimize the use of a simulation
 tool to run efficiently an iterative parallel algorithm in asynchronous 
 mode in a grid architecture. 
 
+\LZK{Perspectives???}
+
 \section*{Acknowledgment}
 
 This work is partially funded by the Labex ACTION program (contract ANR-11-LABX-01-01).
 \todo[inline]{The authors would like to thank\dots{}}
 
-
 % trigger a \newpage just before the given reference
 % number - used to balance the columns on the last page
 % adjust value as needed - may need to be readjusted if
@@ -644,6 +647,8 @@ This work is partially funded by the Labex ACTION program (contract ANR-11-LABX-
 \bibliographystyle{IEEEtran}
 \bibliography{IEEEabrv,hpccBib}
 
+
+
 \end{document}
 
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