Merge branch 'master' of ssh://bilbo.iut-bm.univ-fcomte.fr/rce2015

[rce2015.git] / paper.tex

diff --git a/paper.tex b/paper.tex
index 0d2469420d307d7fc98e6ea7ced52b90d89fe610..5122a8498e4dc14ad126a20249bc6c7e043bece3 100644 (file)
--- a/paper.tex
+++ b/paper.tex
@@ -70,8 +70,8 @@
 
 
 
 
 
 

-\begin{document} \RCE{Titre a confirmer.} \title{Comparative performance
-analysis of simulated grid-enabled numerical iterative algorithms}
+\begin{document}
+\title{Grid-enabled simulation of large-scale linear iterative solvers}

 %\itshape{\journalnamelc}\footnotemark[2]}
 
 \author{Charles Emile Ramamonjisoa\affil{1},
 %\itshape{\journalnamelc}\footnotemark[2]}
 
 \author{Charles Emile Ramamonjisoa\affil{1},


@@ -94,7 +94,7 @@ analysis of simulated grid-enabled numerical iterative algorithms}
   Email:~\email{l.zianekhodja@ulg.ac.be}
 }
 
   Email:~\email{l.zianekhodja@ulg.ac.be}
 }
 

-\begin{abstract}   The behavior of multi-core applications is always a challenge
+\begin{abstract} The behavior of multi-core 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
 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


@@ -102,19 +102,23 @@ 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. 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
 bandwidth, latency, number of processors) and to simulate the execution of such
 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
+help developers to better tune their applications for a given multi-core

 architecture.
 
 architecture.
 

-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 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 simulated
+%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 linear  systems. Two different  variants of
+%the Multisplitting are studied: one  using synchronoous  iterations and  another
+%one  with asynchronous iterations.
+In this paper we focus our attention on the simulation of iterative algorithms to solve sparse linear systems on large clusters. We study the behavior of the widely used GMRES algorithm and two different variants of the Multisplitting algorithms: one using synchronous iterations and another one with asynchronous iterations.  
+For each algorithm we have simulated

 different architecture parameters to evaluate their influence on the overall
 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.
+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.
+The simulations confirm the real results previously obtained on different real multi-core architectures and also confirm the efficiency of the asynchronous Multisplitting algorithm on distant clusters compared to the synchronous GMRES algorithm.

 
 \end{abstract}
 
 
 \end{abstract}
 


@@ -136,7 +140,7 @@ 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,
 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 counterpart, the simulation results need to be consistent with the real ones.
+code debugging, ability to obtain results quickly\dots{} In counterpart, the simulation results need to be consistent with the real ones.

 
 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
 
 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


@@ -165,34 +169,30 @@ 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  a small
 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  a small

-parameter variation of the execution platform can lead to very different numbers
-of iterations to reach the converge and so to very different execution times. In
-this challenging context we think that the  use of a simulation tool can greatly
-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 solvers) 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{saad86} in synchronous mode. 
-
-\LZK{Pas trop convainquant comme argument pour valider l'approche de simulation. \\On peut dire par exemple: on a pu simuler différents algos itératifs à large échelle (le plus connu GMRES et deux variantes de multisplitting) et la simulation nous a permis (sans avoir le vrai matériel) de déterminer quelle serait la meilleure solution pour une telle configuration de l'archi ou vice versa.\\A revoir...}
-
-The obtained results on different
-simulated multi-core architectures confirm the real results previously obtained
-on non simulated architectures.  
-
-\LZK{Il n y a pas dans la partie expé cette comparaison et confirmation des résultats entre la simulation et l'exécution réelle des algos sur les vrais clusters.\\ Sinon on pourrait ajouter dans la partie expé une référence vers le journal supercomput de krylov multi pour confirmer que cette méthode est meilleure que GMRES sur les clusters large échelle.}
-
-We also confirm  the efficiency  of the
-asynchronous  multisplitting algorithm  compared to the synchronous  GMRES. 
-
-\LZK{P.S.: Pour tout le papier, le principal objectif n'est pas de faire des comparaisons entre des méthodes itératives!!\\Sinon, les deux algorithmes Krylov multisplitting synchrone et multisplitting asynchrone sont plus efficaces que GMRES sur des clusters à large échelle.\\Et préciser, si c'est vraiment le cas, que le multisplitting asynchrone est plus efficace et adapté aux clusters distants par rapport aux deux autres algos (je n'ai pas encore lu la partie expé)}
-
-In
-this way and with a simple computing architecture (a laptop) SimGrid allows us
+parameter variation of the execution platform and of the application data can
+lead to very different numbers of iterations to reach the converge and so to
+very different execution times. In this challenging context we think that the
+use of a simulation tool can greatly leverage the possibility of testing various
+platform scenarios.
+
+The  {\bf 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 solvers) 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 Krylov
+multisplitting  algorithm   with  the   GMRES  (Generalized   Minimal  Residual)
+solver~\cite{saad86} in  synchronous mode.  The simulation  results allow  us to
+determine  which method  to choose  given a  specified multi-core  architecture.
+Moreover the  obtained results  on different simulated  multi-core architectures
+confirm the  real results  previously obtained  on non  simulated architectures.
+More precisely the simulated results are in accordance (i.e. with the same order
+of magnitude)  with the works  presented in~\cite{couturier15}, which  show that
+the synchronous  multisplitting method  is more efficient  than GMRES  for large
+scale  clusters.   Simulated   results  also  confirm  the   efficiency  of  the
+asynchronous  multisplitting   algorithm  compared  to  the   synchronous  GMRES
+especially in case of geographically distant clusters.
+
+In this way and with a simple computing architecture (a laptop) SimGrid allows us

 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
 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


@@ -205,8 +205,6 @@ Section~\ref{sec:04} details the different solvers that we use.  Finally our
 experimental results are presented in section~\ref{sec:expe} followed by some
 concluding remarks and perspectives.
 
 experimental results are presented in section~\ref{sec:expe} followed by some
 concluding remarks and perspectives.
 

-\LZK{Proposition d'un titre pour le papier: Grid-enabled simulation of large-scale linear iterative solvers.}
-

 
 \section{The asynchronous iteration model and the motivations of our work}
 \label{sec:asynchro}
 
 \section{The asynchronous iteration model and the motivations of our work}
 \label{sec:asynchro}


@@ -237,7 +235,7 @@ for the asynchronous scheme (this number depends depends on  the delay of the
 messages). Note that, it is not the case in the synchronous mode where the
 number of iterations is the same than in the sequential mode. In this way, the
 set of the parameters  of the  platform (number  of nodes,  power of nodes,
 messages). Note that, it is not the case in the synchronous mode where the
 number of iterations is the same than in the sequential mode. In this way, the
 set of the parameters  of the  platform (number  of nodes,  power of nodes,

-inter and  intra clusters  bandwidth  and  latency \ldots) and  of  the
+inter and  intra clusters  bandwidth  and  latency, \ldots) and  of  the

 application can drastically change the number of iterations required to get the
 convergence. It follows that asynchronous iterative algorithms are difficult to
 optimize since the financial and deployment costs on large scale multi-core
 application can drastically change the number of iterations required to get the
 convergence. It follows that asynchronous iterative algorithms are difficult to
 optimize since the financial and deployment costs on large scale multi-core


@@ -252,6 +250,57 @@ magnitude. To our knowledge, there is no study on this problematic.
 SimGrid~\cite{SimGrid,casanova+legrand+quinson.2008.simgrid,casanova+giersch+legrand+al.2014.versatile} is a discrete event simulation framework to study the behavior of large-scale distributed computing platforms as Grids, Peer-to-Peer systems, Clouds and High Performance Computation systems. It is widely used to simulate and evaluate heuristics, prototype applications or even assess legacy MPI applications. It is still actively developed by the scientific community and distributed as an open source software.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%
 SimGrid~\cite{SimGrid,casanova+legrand+quinson.2008.simgrid,casanova+giersch+legrand+al.2014.versatile} is a discrete event simulation framework to study the behavior of large-scale distributed computing platforms as Grids, Peer-to-Peer systems, Clouds and High Performance Computation systems. It is widely used to simulate and evaluate heuristics, prototype applications or even assess legacy MPI applications. It is still actively developed by the scientific community and distributed as an open source software.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%

+% SimGrid~\cite{SimGrid,casanova+legrand+quinson.2008.simgrid,casanova+giersch+legrand+al.2014.versatile}
+% is a simulation framework to study the behavior of large-scale distributed
+% systems.  As its name suggests, it emanates from the grid computing community,
+% but is nowadays used to study grids, clouds, HPC or peer-to-peer systems.  The
+% early versions of SimGrid date back from 1999, but it is still actively
+% developed and distributed as an open source software.  Today, it is one of the
+% major generic tools in the field of simulation for large-scale distributed
+% systems.
+
+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.  SMPI is the interface that has been used for the work described in
+this paper.  The SMPI interface implements about \np[\%]{80} of the MPI 2.0
+standard~\cite{bedaride+degomme+genaud+al.2013.toward}, and supports
+applications written in C or Fortran, with little or no modifications (cf Section IV - paragraph B).
+
+Within SimGrid, the execution of a distributed application is simulated by a
+single process.  The application code is really executed, but some operations,
+like communications, are intercepted, and their running time is computed
+according to the characteristics of the simulated execution platform.  The
+description of this target platform is given as an input for the execution, by
+means of an XML file.  It describes the properties of the platform, such as
+the computing nodes with their computing power, the interconnection links with
+their bandwidth and latency, and the routing strategy.  The scheduling of the
+simulated processes, as well as the simulated running time of the application
+are computed according to these properties.
+
+To compute the durations of the operations in the simulated world, and to take
+into account resource sharing (e.g. bandwidth sharing between competing
+communications), SimGrid uses a fluid model.  This allows users to run relatively fast
+simulations, while still keeping accurate
+results~\cite{bedaride+degomme+genaud+al.2013.toward,
+  velho+schnorr+casanova+al.2013.validity}.  Moreover, depending on the
+simulated application, SimGrid/SMPI allows to skip long lasting computations and
+to only take their duration into account.  When the real computations cannot be
+skipped, but the results are unimportant for the simulation results, it is
+also possible to share dynamically allocated data structures between
+several simulated processes, and thus to reduce the whole memory consumption.
+These two techniques can help to run simulations on a very large scale.
+
+The validity of simulations with SimGrid has been asserted by several studies.
+See, for example, \cite{velho+schnorr+casanova+al.2013.validity} and articles
+referenced therein for the validity of the network models.  Comparisons between
+real execution of MPI applications on the one hand, and their simulation with
+SMPI on the other hand, are presented in~\cite{guermouche+renard.2010.first,
+  clauss+stillwell+genaud+al.2011.single,
+  bedaride+degomme+genaud+al.2013.toward}.  All these works conclude that
+SimGrid is able to simulate pretty accurately the real behavior of the
+applications.

 %%%%%%%%%%%%%%%%%%%%%%%%%
 
 \section{Two-stage multisplitting methods}
 %%%%%%%%%%%%%%%%%%%%%%%%%
 
 \section{Two-stage multisplitting methods}


@@ -522,7 +571,8 @@ architectures and scaling up the input matrix size}
  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}
  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}

-\caption{Test conditions: various grid configurations with the input matix size N$_{x}$=150 or N$_{x}$=170 \RC{N2 n'est pas défini..}\RC{Nx est défini, Ny? Nz?}}
+\caption{Test conditions: various grid configurations with the input matix size N$_{x}$=150 or N$_{x}$=170 \RC{N2 n'est pas défini..}\RC{Nx est défini, Ny? Nz?}
+\AG{La lettre 'x' n'est pas le symbole de la multiplication. Utiliser \texttt{\textbackslash times}.  Idem dans le texte, les figures, etc.}}

 \label{tab:01}
 \end{center}
 \end{table}
 \label{tab:01}
 \end{center}
 \end{table}


@@ -545,7 +595,8 @@ multisplitting method.
   \begin{center}
     \includegraphics[width=100mm]{cluster_x_nodes_nx_150_and_nx_170.pdf}
   \end{center}
   \begin{center}
     \includegraphics[width=100mm]{cluster_x_nodes_nx_150_and_nx_170.pdf}
   \end{center}

-  \caption{Various grid configurations with the input matrix size N$_{x}$=150 and N$_{x}$=170\RC{idem}}
+  \caption{Various grid configurations with the input matrix size N$_{x}$=150 and N$_{x}$=170\RC{idem}
+\AG{Utiliser le point comme séparateur décimal et non la virgule.  Idem dans les autres figures.}}

   \label{fig:01}
 \end{figure}
 
   \label{fig:01}
 \end{figure}
 


@@ -578,16 +629,15 @@ speed inter-cluster  network (N1) and  also on  a less performant  network (N2).
 Figure~\ref{fig:02} shows that end users will reduce the execution time
 for  both  algorithms when using  a  grid  architecture  like  4x16 or  8x8: the reduction is about $2$. The results depict  also that when
 the  network speed  drops down (variation of 12.5\%), the  difference between  the two Multisplitting algorithms execution times can reach more than 25\%.
 Figure~\ref{fig:02} shows that end users will reduce the execution time
 for  both  algorithms when using  a  grid  architecture  like  4x16 or  8x8: the reduction is about $2$. The results depict  also that when
 the  network speed  drops down (variation of 12.5\%), the  difference between  the two Multisplitting algorithms execution times can reach more than 25\%.

-%\RC{c'est pas clair : la différence entre quoi et quoi?}
-%\DL{pas clair}
-%\RCE{Modifie}
+

 
 
 %\begin{wrapfigure}{l}{100mm}
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{cluster_x_nodes_n1_x_n2.pdf}
 
 
 %\begin{wrapfigure}{l}{100mm}
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{cluster_x_nodes_n1_x_n2.pdf}

-\caption{Grid 2x16 and 4x8 with networks N1 vs N2}
+\caption{Grid 2x16 and 4x8 with networks N1 vs N2
+\AG{\np{8E-6}, \np{5E-6} au lieu de 8E-6, 5E-6}}

 \label{fig:02}
 \end{figure}
 %\end{wrapfigure}
 \label{fig:02}
 \end{figure}
 %\end{wrapfigure}


@@ -612,7 +662,8 @@ the  network speed  drops down (variation of 12.5\%), the  difference between  t
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{network_latency_impact_on_execution_time.pdf}
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{network_latency_impact_on_execution_time.pdf}

-\caption{Network latency impacts on execution time}
+\caption{Network latency impacts on execution time
+\AG{\np{E-6}}}

 \label{fig:03}
 \end{figure}
 
 \label{fig:03}
 \end{figure}
 


@@ -646,7 +697,8 @@ magnitude with a latency of $8.10^{-6}$.
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{network_bandwith_impact_on_execution_time.pdf}
 \begin{figure} [ht!]
 \centering
 \includegraphics[width=100mm]{network_bandwith_impact_on_execution_time.pdf}

-\caption{Network bandwith impacts on execution time}
+\caption{Network bandwith impacts on execution time
+\AG{``Execution time'' avec un 't' minuscule}. Idem autres figures.}

 \label{fig:04}
 \end{figure}
 
 \label{fig:04}
 \end{figure}
 


@@ -722,10 +774,16 @@ on the  algorithms performance in  varying the CPU  power of the  clusters nodes
 from $1$ to $19$ GFlops.  The outputs  depicted in Figure~\ref{fig:06}  confirm the
 performance gain,  around $95\%$ for  both of the  two methods, after  adding more
 powerful CPU.
 from $1$ to $19$ GFlops.  The outputs  depicted in Figure~\ref{fig:06}  confirm the
 performance gain,  around $95\%$ for  both of the  two methods, after  adding more
 powerful CPU.

+\ \\
+%\DL{il faut une conclusion sur ces tests : ils confirment les résultats déjà
+%obtenus en grandeur réelle. Donc c'est une aide précieuse pour les dev. Pas
+%besoin de déployer sur une archi réelle}

 
 

-\DL{il faut une conclusion sur ces tests : ils confirment les résultats déjà
-obtenus en grandeur réelle. Donc c'est une aide précieuse pour les dev. Pas
-besoin de déployer sur une archi réelle}
+To conclude these series of experiments, with  SimGrid we have been able to make
+many simulations  with many parameters  variations. Doing all  these experiments
+with a real platform is most of  the time not possible. Moreover the behavior of
+both GMRES and  Krylov multisplitting methods is in accordance  with larger real
+executions on large scale supercomputer~\cite{couturier15}.

 
 
 \subsection{Comparing GMRES in native synchronous mode and the multisplitting algorithm in asynchronous mode}
 
 
 \subsection{Comparing GMRES in native synchronous mode and the multisplitting algorithm in asynchronous mode}


@@ -772,7 +830,7 @@ Again,  comprehensive and  extensive tests  have been  conducted with  different
 parameters as  the CPU power, the  network parameters (bandwidth and  latency)
 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
 parameters as  the CPU power, the  network parameters (bandwidth and  latency)
 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{fig:07}  are  reported the  best  grid  configurations allowing
+Table~\ref{tab:08}  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
 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


@@ -787,7 +845,7 @@ geographically distant clusters through the internet.
     \end{tabular}}
 
 
     \end{tabular}}
 
 

-\begin{figure}[!t]
+\begin{table}[!t]

 \centering
 %\begin{table}
 %  \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}
 \centering
 %\begin{table}
 %  \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}


@@ -815,8 +873,8 @@ geographically distant clusters through the internet.
   \end{mytable}
 %\end{table}
  \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}
   \end{mytable}
 %\end{table}
  \caption{Relative gain of the multisplitting algorithm compared with the classical GMRES}

- \label{fig:07}
-\end{figure}
+ \label{tab:08}
+\end{table}

 
 
 \section{Conclusion}
 
 
 \section{Conclusion}


@@ -830,6 +888,7 @@ This work is partially funded by the Labex ACTION program (contract ANR-11-LABX-
 \bibliographystyle{wileyj}
 \bibliography{biblio}
 
 \bibliographystyle{wileyj}
 \bibliography{biblio}
 

+

 \end{document}
 
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