X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/rce2015.git/blobdiff_plain/f2509eae84a623fa2e4d8ce48287c665efb02f9d..f721cbed7d2388830aaa885dc59b8a9bab852a32:/paper.tex?ds=inline

diff --git a/paper.tex b/paper.tex
index f800225..87949b4 100644
--- a/paper.tex
+++ b/paper.tex
@@ -92,9 +92,18 @@
 %% Lilia Ziane Khodja: Department of Aerospace \& Mechanical Engineering\\ Non Linear Computational Mechanics\\ University of Liege\\ Liege, Belgium. Email: l.zianekhodja@ulg.ac.be
 
 \begin{abstract}
-  The behavior of multicore applications is always a challenge to predict, especially with a new architecture for which no experiment has been performed. With some applications, it is difficult, if not impossible, to build accurate performance models. That is why another solution is to use a simulation tools that allows us to change many parameters of the architecture (network bandwidth, latency, number of processors) and to simulate the execution of such applications.
+  The behavior of multicore applications is always a challenge to predict, especially with a new architecture for which no experiment has been performed. With some applications, it is difficult, if not impossible, to build 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.
 
-  In this paper, we focus our attention on two parallel iterative algorithms: one with synchronoous iterations and another one with asynchronous iterations.
+In this paper, 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  variantsof 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.
+
+  
 
   
 \end{abstract}
@@ -104,6 +113,47 @@
 \maketitle
 
 \section{Introduction} 
+The use of multi-core architectures for solving large scientific problems seems to  become imperative  in  a  lot  of  cases. 
+Whatever the scale of these architectures (distributed clusters, computational grids, embedded multi-core \ldots) they  are generally 
+well adapted to execute complexe parallel applications operating on a large amount of data.  Unfortunately,  users (industrials or scientists), 
+who need such computational resources may not have an easy access to such efficient architectures. The cost of using the platform and/or the cost of 
+testing and deploying an application are often very important.  So, in this context it is difficult to optimize a given application for a given 
+architecture. In this way and in order to reduce the access cost to these computing resources it seems very interesting to use a simulation environment. 
+The advantages are numerous: development life cycle, code debugging, ability to obtain results quickly \ldots
+
+In this paper we focus on a class of highly efficient parallel algorithms called \emph{iterative algorithms}. The
+parallel scheme of iterative methods is quite simple. It generally involves the division of the problem
+into  several  \emph{blocks}  that  will  be  solved  in  parallel  on  multiple
+processing units.  Then each processing unit has to
+compute an iteration, to send/receive some data dependencies to/from
+its neighbors and to iterate this process until the convergence of
+the method. Several well-known methods demonstrate the convergence of these algorithms~\cite{BT89,Bahi07}.
+In this processing mode a task cannot begin a new iteration while it
+has not received data dependencies from its neighbors. We say that the iteration computation follows a synchronous scheme.
+In the asynchronous scheme a task can compute a new iteration without having to
+wait for the data dependencies coming from its neighbors. Both
+communication and computations are asynchronous inducing that there is
+no more idle times, due to synchronizations, between two
+iterations~\cite{bcvc06:ij}. This model presents some advantages and drawbacks that we detail in section 2 but even if the number of iterations required to converge is 
+generally  greater  than for the synchronous  case, it appears that the asynchronous  iterative scheme  can significantly  reduce  overall execution
+times by  suppressing idle  times due to  synchronizations~\cite{Bahi07} for more details.
+
+Nevertheless, in both cases (synchronous or asynchronous) it is very time consuming to find optimal configuration and deployment requirements 
+for a given application on a given multi-core architecture. Finding good resource allocations policies under varying CPU power, network speeds and 
+loads is very challenging and labor intensive.~\cite{Calheiros:2011:CTM:1951445.1951450}.   This problematic is even more difficult for the asynchronous scheme 
+where variations of the parameters of the execution platform can lead to very different number of iterations required to converge and so to very different execution times.
+In this challenging context we think that the use of a simulation tool can leverage the possibility of testing various platform scenarios.
+
+The main contribution of this paper is to show that the use of a simulation tool (i.e. the SimGrid   toolkit~\cite{SimGrid}) in the context of real 
+parallel applications (i.e. large linear system solver) can help developers to better tune their application for a given multi-core architecture.
+To show the validity of this approach we first compare the simulated execution of the multisplitting algorithm  with  the  GMRES   (Generalized   Minimal  Residual) solver
+\cite{ref1} both in synchronous mode. The obtained results on different simulated multi-core architectures confirm the results previously obtained on non simulated architecture. 
+We also confirm  the efficiency  of the  asynchronous  multisplitting algorithm  comparing to the synchronous  GMRES. In this way and with a simple computing architecture (a laptop) 
+SimGrid allows us (with small modifications of the MPI code) to run a test campaign  of  a  real parallel iterative  applications on  different simulated multi-core architectures. 
+To our knowledge, there is no related work on the large-scale multi-core simulation of a real synchronous and asynchronous iterative application.  
+
+This paper is organized as follows:
+
 
 \section{The asynchronous iteration model}
 
@@ -200,17 +250,17 @@ The algorithm in Figure~\ref{alg:02} includes the procedure of the residual mini
 \subsection{Simulation of two-stage methods using SimGrid framework}
 \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 test reproducibility under the same conditions.According our experience, very few modifications are required to adapt a MPI program to run in SIMGRID simulator using SMPI (Simulator MPI).The first modification is to include SMPI libraries and related header files (smpi.h). The second and important modification is to eliminate all global variables in moving them to local subroutine 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 the Simgrid to simulate the grid environment.The last modification on the MPI program pointed out for some cases, the review of the sequence of the MPI\_Isend, MPI\_Irecv and MPI\_Waitall instructions which might cause an infinite loop.     
+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 test reproducibility under the same conditions. According our experience, very few modifications are required to adapt a MPI program to run in SIMGRID simulator using SMPI (Simulator MPI).The first modification is to include SMPI libraries and related header files (smpi.h). The second and important modification is to eliminate all global variables in moving them to local subroutine 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 the Simgrid to simulate the grid environment.The last modification on the MPI program pointed out for some cases, the review of the sequence of the MPI\_Isend, MPI\_Irecv and MPI\_Waitall instructions which might cause an infinite loop.     
 
 
 \paragraph{SIMGRID Simulator parameters}
 
 \begin{itemize}
-	\item HOSTFILE: Hosts description file.
-	\item PLATFORM: File describing the platform architecture : clusters (CPU power,
+	\item hostfile: Hosts description file.
+	\item plarform: File describing the platform architecture : clusters (CPU power,
 \dots{}), intra cluster network description, inter cluster network (bandwidth bw,
-lat latency, \dots{}).
-	\item ARCHI   : Grid computational description (Number of clusters, Number of 
+latency lat, \dots{}).
+	\item archi   : Grid computational description (Number of clusters, Number of 
 nodes/processors for each cluster). 
 \end{itemize}
 
@@ -220,43 +270,38 @@ In addition, the following arguments are given to the programs at runtime:
 \begin{itemize}
 	\item Maximum number of inner and outer iterations;
 	\item Inner and outer precisions;
-	\item Matrix size (NX, NY and NZ);
+	\item Matrix size (N$_{x}$, N$_{y}$ and N$_{z}$);
 	\item Matrix diagonal value = 6.0;
 	\item Execution Mode: synchronous or asynchronous.
 \end{itemize}
 
-At last, note that the two solver algorithms have been executed with the Simgrid selector --cfg=smpi/running\_power which determine the computational power (here 19GFlops) of the simulator host machine.  
+At last, note that the two solver algorithms have been executed with the Simgrid selector -cfg=smpi/running\_power which determine the computational power (here 19GFlops) of the simulator host machine.  
 
 %%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%
 
-\section{Experimental, Results and Comments}
+\section{Experimental Results}
 
 
 \subsection{Setup study and Methodology}
 
 To conduct our study, we have put in place the following methodology 
-which can be reused with any grid-enabled applications.
+which can be reused for any grid-enabled applications.
 
 \textbf{Step 1} : Choose with the end users the class of algorithms or 
 the application to be tested. Numerical parallel iterative algorithms 
-have been chosen for the study in the paper. 
+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 three variants algorithms for the 
-resolution of three 3D-Poisson problem: (1) using the classical GMRES alias Algo-1 in this 
-paper, (2) using the multisplitting method alias Algo-2 and (3) an 
-enhanced version of the multisplitting method as Algo-3. In addition, 
-SIMGRID simulator has been chosen to simulate the behaviors of the 
-distributed applications. SIMGRID is running on the Mesocentre 
-datacenter in Franche-Comte University but also in a virtual 
-machine on a laptop.
+experimentation. In our case, we have two variants algorithms for the 
+resolution of three 3D-Poisson problem: (1) using the classical GMRES (Algo-1)(2) and the multisplitting method (Algo-2). In addition, SIMGRID simulator has been chosen to simulate the behaviors of the 
+distributed applications. SIMGRID is running on the Mesocentre datacenter in Franche-Comte University but also in a virtual machine on a 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 
 in one hand the algorithm execution mode (synchronous and asynchronous) 
 and in the other hand the execution time and the number of iterations of 
-the application before obtaining the convergence.
+the application before obtaining the convergence. \\
 
 \textbf{Step 4 }: Setup up the different grid testbeds environment 
 which will be simulated in the simulator tool to run the program. The 
@@ -265,15 +310,15 @@ grid containing 2 clusters with 16 hosts (processors/cores) each -, 4x8,
 4x16, 8x8 and 2x50. The network has been designed to operate with a 
 bandwidth equals to 10Gbits (resp. 1Gbits/s) and a latency of 8E-6 
 microseconds (resp. 5E-5) for the intra-clusters links (resp. 
-inter-clusters backbone links).
+inter-clusters backbone links). \\
 
-\textbf{Step 5}: Process an extensive and comprehensive testings 
+\textbf{Step 5}: Conduct an extensive and comprehensive testings 
 within these configurations in varying the key parameters, especially 
 the CPU power capacity, the network parameters and also the size of the 
-input matrix. Note that some parameters should be invariant to allow the 
-comparison like some program input arguments.
+input matrix. Note that some parameters should be fixed to be invariant to allow the 
+comparison like some program input arguments. \\
 
-{Step 6} : Collect and analyze the output results.
+\textbf{Step 6} : Collect and analyze the output results.
 
 \subsection{Factors impacting distributed applications performance in 
 a grid environment}
@@ -318,7 +363,7 @@ In the scope of this paper, our first objective is to demonstrate the
 Algo-2 (Multisplitting method) shows a better performance in grid 
 architecture compared with Algo-1 (Classical GMRES) both running in 
 \textbf{\textit{synchronous mode}}. Better algorithm performance 
-should mean a less number of iterations output and a less execution time 
+should means a less number of iterations output and a less execution time 
 before reaching the convergence. For a systematic study, the experiments 
 should figure out that, for various grid parameters values, the 
 simulator will confirm the targeted outcomes, particularly for poor and 
@@ -326,7 +371,7 @@ slow networks, focusing on the impact on the communication performance
 on the chosen class of algorithm.
 
 The following paragraphs present the test conditions, the output results 
-and our comments.
+and our comments.\\
 
 
 \textit{3.a Executing the algorithms on various computational grid 
@@ -338,11 +383,11 @@ architecture scaling up the input matrix size}
 \begin{tabular}{r c }
  \hline  
  Grid & 2x16, 4x8, 4x16 and 8x8\\ %\hline
- Network & N2 : bw=1Gbs-lat=5E-05 \\ %\hline
- Input matrix size & N$_{x}$ =150 x 150 x 150 and\\ %\hline
- - & N$_{x}$ =170 x 170 x 170    \\ \hline
+ Network & N2 : bw=1Gbits/s - lat=5.10$^{-5}$ \\ %\hline
+ Input matrix size & N$_{x}$ x N$_{y}$ x N$_{z}$ =150 x 150 x 150\\ %\hline
+ - &  N$_{x}$ x N$_{y}$ x N$_{z}$  =170 x 170 x 170    \\ \hline
  \end{tabular}
-Table 1 : Clusters x Nodes with NX=150 or NX=170 \\
+Table 1 : Clusters x Nodes with N$_{x}$=150 or N$_{x}$=170 \\
 
 \end{footnotesize}
 
@@ -351,7 +396,7 @@ Table 1 : Clusters x Nodes with NX=150 or NX=170 \\
 %\RCE{J'ai voulu mettre les tableaux des donnÃ©es mais je pense que c'est inutile et Ã§a va surcharger}
 
 
-The results in figure 1 show the non-variation of the number of 
+The results in figure 3 show the non-variation of the number of 
 iterations of classical GMRES for a given input matrix size; it is not 
 the case for the multisplitting method. 
 
@@ -359,7 +404,7 @@ the case for the multisplitting method.
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{cluster_x_nodes_nx_150_and_nx_170.pdf}
-\caption{Cluster x Nodes NX=150 and NX=170} 
+\caption{Cluster x Nodes N$_{x}$=150 and N$_{x}$=170} 
 %\label{overflow}}
 \end{figure}
 %\end{wrapfigure}
@@ -379,9 +424,9 @@ matrix size.
 \begin{tabular}{r c }
  \hline  
  Grid & 2x16, 4x8\\ %\hline
- Network & N1 : bw=10Gbs-lat=8E-06 \\ %\hline
- - & N2 : bw=1Gbs-lat=5E-05 \\
- Input matrix size & N$_{x}$ =150 x 150 x 150\\ \hline \\
+ Network & N1 : bw=10Gbs-lat=8.10$^{-6}$ \\ %\hline
+ - & N2 : bw=1Gbs-lat=5.10$^{-5}$ \\
+ Input matrix size & N$_{x}$ x N$_{y}$ x N$_{z}$ =150 x 150 x 150\\ \hline \\
  \end{tabular}
 Table 2 : Clusters x Nodes - Networks N1 x N2 \\
 
@@ -399,8 +444,8 @@ Table 2 : Clusters x Nodes - Networks N1 x N2 \\
 %\end{wrapfigure}
 
 The experiments compare the behavior of the algorithms running first on 
-speed inter- cluster network (N1) and a less performant network (N2). 
-The figure 2 shows that end users will gain to reduce the execution time 
+a speed inter- cluster network (N1) and a less performant network (N2). 
+Figure 4 shows that end users will gain to reduce the execution time 
 for both algorithms in using a grid architecture like 4x16 or 8x8: the 
 performance was increased in a factor of 2. The results depict also that 
 when the network speed drops down, the difference between the execution 
@@ -414,9 +459,8 @@ times can reach more than 25\%.
  \hline  
  Grid & 2x16\\ %\hline
  Network & N1 : bw=1Gbs \\ %\hline
- Input matrix size & N$_{x}$ =150 x 150 x 150\\ \hline\\
+ Input matrix size & N$_{x}$ x N$_{y}$ x N$_{z}$ =150 x 150 x 150\\ \hline\\
  \end{tabular}
-
 Table 3 : Network latency impact \\
 
 \end{footnotesize}
@@ -431,12 +475,12 @@ Table 3 : Network latency impact \\
 \end{figure}
 
 
-According the results in table and figure 3, degradation of the network 
+According the results in figure 5, degradation of the network 
 latency from 8.10$^{-6}$ to 6.10$^{-5}$ implies an absolute time 
 increase more than 75\% (resp. 82\%) of the execution for the classical 
 GMRES (resp. multisplitting) algorithm. In addition, it appears that the 
 multisplitting method tolerates more the network latency variation with 
-a less rate increase. Consequently, in the worst case (lat=6.10$^{-5
+a less rate increase of the execution time. Consequently, in the worst case (lat=6.10$^{-5
 }$), the execution time for GMRES is almost the double of the time for 
 the multisplitting, even though, the performance was on the same order 
 of magnitude with a latency of 8.10$^{-6}$. 
@@ -448,10 +492,9 @@ of magnitude with a latency of 8.10$^{-6}$.
 \begin{tabular}{r c }
  \hline  
  Grid & 2x16\\ %\hline
- Network & N1 : bw=1Gbs - lat=5E-05 \\ %\hline
- Input matrix size & N$_{x}$ =150 x 150 x 150\\ \hline
+ Network & N1 : bw=1Gbs - lat=5.10$^{-5}$ \\ %\hline
+ Input matrix size & N$_{x}$ x N$_{y}$ x N$_{z}$ =150 x 150 x 150\\ \hline \\
  \end{tabular}
-
 Table 4 : Network bandwidth impact \\
 
 \end{footnotesize}
@@ -468,7 +511,7 @@ Table 4 : Network bandwidth impact \\
 
 The results of increasing the network bandwidth depict the improvement 
 of the performance by reducing the execution time for both of the two 
-algorithms. However, and again in this case, the multisplitting method 
+algorithms (Figure 6). However, and again in this case, the multisplitting method 
 presents a better performance in the considered bandwidth interval with 
 a gain of 40\% which is only around 24\% for classical GMRES.
 
@@ -479,8 +522,8 @@ a gain of 40\% which is only around 24\% for classical GMRES.
 \begin{tabular}{r c }
  \hline  
  Grid & 4x8\\ %\hline
- Network & N2 : bw=1Gbs - lat=5E-05 \\ %\hline
- Input matrix size & N$_{x}$ = From 40 to 200\\ \hline
+ Network & N2 : bw=1Gbs - lat=5.10$^{-5}$ \\ %\hline
+ Input matrix size & N$_{x}$ = From 40 to 200\\ \hline \\
  \end{tabular}
 Table 5 : Input matrix size impact\\
 
@@ -495,14 +538,14 @@ Table 5 : Input matrix size impact\\
 \end{figure}
 
 In this experimentation, the input matrix size has been set from 
-Nx=Ny=Nz=40 to 200 side elements that is from 40$^{3}$ = 64.000 to 
-200$^{3}$ = 8.000.000 points. Obviously, as shown in the figure 5, 
-the execution time for the algorithms convergence increases with the 
-input matrix size. But the interesting result here direct on (i) the 
+N$_{x}$ = N$_{y}$ = N$_{z}$ = 40 to 200 side elements that is from 40$^{3}$ = 64.000 to 
+200$^{3}$ = 8.000.000 points. Obviously, as shown in the figure 7, 
+the execution time for the two algorithms convergence increases with the 
+input matrix size. But the interesting results here direct on (i) the 
 drastic increase (300 times) of the number of iterations needed before 
 the convergence for the classical GMRES algorithm when the matrix size 
-go beyond Nx=150; (ii) the classical GMRES execution time also almost 
-the double from Nx=140 compared with the convergence time of the 
+go beyond N$_{x}$=150; (ii) the classical GMRES execution time also almost 
+the double from N$_{x}$=140 compared with the convergence time of the 
 multisplitting method. These findings may help a lot end users to setup 
 the best and the optimal targeted environment for the application 
 deployment when focusing on the problem size scale up. Note that the 
