Reste la partie gridification

[gpc2011.git] / gpc2011.tex

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\begin{document}

\title{Gridification of a Radiotherapy Dose Computation Application with the XtremWeb-CH Environment}


\author{Nabil Abdennhader\inst{1} \and Mohamed Ben Belgacem{1} \and Raphaël Couturier\inst{2} \and
  David Laiymani\inst{2} \and Sébastien  Miquée\inst{2} \and Marko Niinimaki\inst{1} \and Marc Sauget\inst{2}}

\institute{
University of Applied Sciences Western Switzerland, hepia Geneva,
Switzerland \\
\email{nabil.abdennadher@hesge.ch, mohamed.benbelgacem@unige.ch, markopekka.niinimaeki@hesge.ch}
\and
Laboratoire d'Informatique de l'universit\'{e}
  de Franche-Comt\'{e} \\
  IUT Belfort-Montbéliard, Rue Engel Gros, 90016 Belfort - France \\
\email{raphael.couturier, david.laiymani, sebastien.miquee@univ-fcomte.fr}
\and
 FEMTO-ST, ENISYS/IRMA, F-25210 Montb\'{e}liard , FRANCE\\
\email{marc.sauget@femtost.fr}
}


\maketitle

\begin{abstract} 
  This paper presents the design and the evaluation of the
  gridification of a radiotherapy dose computation application. Due to
  the inherent characteristics of the application and its execution,
  we choose the architectural context of global (or volunteer) computing.
  For this, we used the XtremWeb-CH environement. Experiments were
  conducted on a real global computing testbed and show good speed-ups
  and very acceptable platform overhead.  
\end{abstract}


%-------------INTRODUCTION--------------------
\section{Introduction}

The use of distributed architectures for solving large scientific
problems seems to become mandatory in a lot of cases. For example, in
the domain of radiotherapy dose computation the problem is
crucial. The main goal of external beam radiotherapy is the treatment
of tumors while minimizing exposure to healthy tissue. Dosimetric
planning has to be carried out in order to optimize the dose
distribution within the patient. Thus, to determine the most accurate
dose distribution during treatment planning, a compromise must be
found between the precision and the speed of calculation. Current
techniques, using analytic methods, models and databases, are rapid
but lack precision. Enhanced precision can be achieved by using
calculation codes based, for example, on Monte Carlo methods. The main
drawback of these methods is their computation times which can be
rapidly be huge. In [] the authors proposed a novel approach, called
Neurad, using neural networks. This approach is based on the
collaboration of computation codes and multi-layer neural networks
used as universal approximators. It provides a fast and accurate
evaluation of radiation doses in any given environment for given
irradiation parameters. As the learning step is often very time
consuming, in \cite{bcvsv08:ip} the authors proposed a parallel
algorithm that enable to decompose the learning domain into
subdomains. The decomposition has the advantage to significantly
reduce the complexity of the target functions to approximate.

Now, as there exist several classes of distributed/parallel
architectures (supercomputers, clusters, global computing...)  we have
to choose the best suited one for the parallel Neurad application.
The Global or Volunteer Computing model seems to be an interesting
approach. Here, the computing power is obtained by aggregating unused
(or volunteer) public resources connected to the Internet. For our
case, we can imagine for example, that a part of the architecture will
be composed of some of the different computers of the hospital. This
approach present the advantage to be clearly cheaper than a more
dedicated approach like the use of supercomputers or clusters.

The aim of this paper is to propose and evaluate a gridification of
the Neurad application (more precisely, of the most time consuming
part, the learning step) using a Global Computing approach. For this,
we focus on the XtremWeb-CH environment []. We choose this environment
because it tackles the centralized aspect of other global computing
environments such as XtremWeb [] or Seti []. It tends to a
peer-to-peer approach by distributing some components of the
architecture. For instance, the computing nodes are allowed to
directly communicate. Experiments were conducted on a real Global
Computing testbed. The results are very encouraging. They exhibit an
interesting speed-up and show that the overhead induced by the use of
XtremWeb-CH is very acceptable.

The paper is organized as follows. In Section 2 we present the Neurad
application and particularly it most time consuming part i.e. the
learning step. Section 3 details the XtremWeb-CH environment and
Section 4 exposes the gridification of the Neurad
application. Experimental results are presented in Section 5 and we
end in Section 6 by some concluding remarks and perspectives.

\section{The Neurad application}

\begin{figure}[http]
  \centering
  \includegraphics[width=0.7\columnwidth]{figures/neurad.pdf}
  \caption{The Neurad project}
  \label{f_neurad}
\end{figure}

The \emph{Neurad}~\cite{Neurad} project presented in this paper takes
place in a multi-disciplinary project, involving medical physicists
and computer scientists whose goal is to enhance the treatment
planning of cancerous tumors by external radiotherapy. In our
previous works~\cite{RADIO09,ICANN10,NIMB2008}, we have proposed an
original approach to solve scientific problems whose accurate modeling
and/or analytical description are difficult. That method is based on
the collaboration of computational codes and neural networks used as
universal interpolator. Thanks to that method, the \emph{Neurad}
software provides a fast and accurate evaluation of radiation doses in
any given environment (possibly inhomogeneous) for given irradiation
parameters. We have shown in a previous work (\cite{AES2009}) the
interest to use a distributed algorithm for the neural network
learning. We use a classical RPROP algorithm with a HPU topology to do
the training of our neural network.

Figure~\ref{f_neurad} presents the {\it{Neurad}} scheme. Three parts
are clearly independent: the initial data production, the learning
process and the dose deposit evaluation. The first step, the data
production, is outside the {\it{Neurad}} project. They are many
solutions to obtain data about the radiotherapy treatments like the
measure or the simulation. The only essential criterion is that the
result must be obtain in a homogeneous environment. 

% We have chosen to
% use only a Monte Carlo simulation because this kind of tool is the
% reference in the radiotherapy domains. The advantages to use data
% obtained with a Monte Carlo simulator are the following: accuracy,
% profusion, quantified error and regularity of measure points. But,
% there exist also some disagreements and the most important is the
% statistical noise, forcing a data post treatment. Figure~\ref{f_tray}
% presents the general behavior of a dose deposit in water.


% \begin{figure}[http]
%   \centering
%   \includegraphics[width=0.7\columnwidth]{figures/testC.pdf}
%   \caption{Dose deposit by a photon beam  of 24 mm of width in water (normalized value).}
%   \label{f_tray}
% \end{figure}

The secondary stage of the {\it{Neurad}} project is the learning step
and this is the most time consuming step. This step is off-line but it
is important to reduce the time used for the learning process to keep
a workable tool. Indeed, if the learning time is too huge (for the
moment, this time could reach one week for a limited domain), this
process should not be launched at any time, but only when a major
modification occurs in the environment, like a change of context for
instance. However, it is interesting to update the knowledge of the
neural network, by using the learning process, when the domain evolves
(evolution in material used for the prosthesis or evolution on the
beam (size, shape or energy)). The learning time is related to the
volume of data who could be very important in a real medical context.
A work has been done to reduce this learning time with the
parallelization of the learning process by using a partitioning method
of the global dataset. The goal of this method is to train many neural
networks on sub-domains of the global dataset. After this training,
the use of these neural networks all together allows to obtain a
response for the global domain of study.


\begin{figure}[h]
  \centering
  \includegraphics[width=0.5\columnwidth]{figures/overlap.pdf}
  \caption{Overlapping for a sub-network  in a two-dimensional domain with ratio
    $\alpha$.}
  \label{fig:overlap}
\end{figure}


However, performing the learning on sub-domains constituting a
partition of the initial domain is not satisfying according to the
quality of the results. This comes from the fact that the accuracy of
the approximation performed by a neural network is not constant over
the learned domain. Thus, it is necessary to use an overlapping of
the sub-domains. The overall principle is depicted in
Figure~\ref{fig:overlap}. In this way, each sub-network has an
exploitation domain smaller than its training domain and the
differences observed at the borders are no longer relevant.
Nonetheless, in order to preserve the performance of the parallel
algorithm, it is important to carefully set the overlapping ratio
$\alpha$. It must be large enough to avoid the border's errors, and
as small as possible to limit the size increase of the data subsets.



\section{The XtremWeb-CH environment}
\input{xwch.tex}

\section{}

\label{sec:neurad_gridif}


The Neurad application can be divided into three parts. The first one
aims at dividing data representing dose distribution on an area. This
area contains various parameters, like the density of the medium and
its nature. Multiple ``views'' can be superposed in order to obtain a
more accurate learning. The second part of the application is the
learning itself. This is the most time consuming part and therefore
this is the one which has been ported to XWCH. This part fits well
with the model of the middleware -- all learning tasks execute in
parallel independently with their own local data part, with no
communication, following the fork-join model. As described on Figure
\ref{fig:neurad_grid}, we first send the learning application and data
to the middleware (more precisely on warehouses (DW)) and create the
computation module. When a worker (W) is ready to compute, it requests
a task to execute to the coordinator (Coord.). This latter assigns it
a task. The worker retrieves the application and its assigned data,
and can start the computation. At the end of the learning process, it
sends the result, a weighted neural network which will be used in a
dose distribution process, to a warehouse. The last step of the
application is to retrieve these results and exploit them.


\begin{figure}[ht]
  \centering
  \includegraphics[width=\linewidth]{neurad_gridif}
  \caption{Neurad gridification}
  \label{fig:neurad_grid}
\end{figure}

\section{Experimental results}

\label{sec:neurad_xp}

\subsubsection{Conditions}
\label{sec:neurad_cond}


The evaluation of the execution of the Neurad application on XWCH was
composed as follows. The size of the input data is about 2.4Gb. This
amount of data can be divided into 25 parts – otherwise, data noise
appears and will disturb the learning. We have used 25 computers (XWCH
workers) to execute this part of the application. This generates input
data parts of about 15Mb (in a compressed format). The output data,
which are retrieved after the process, are about 30Kb for each part. We
used two distincts deployments of XWCH. In the first one, the XWCH
coordinator and the warehouses were situated in Geneva, Switzerland
while the workers were running in the same local cluster in Belfort,
France. The second deployment is a local deployment where both
coordinator, warehouses and workers were in the same local cluster.
During the day these machines were used by students of the Computer
Science Department of the IUT of Belfort.

We have furthermore compared the execution of the Neurad application
with and without the XWCH platform in order to measure the overhead
induced by the use of the platform. By "without XWCH" we mean that the
testbed consists only in workers deployed with their respective data by
the use of shell scripts. No specific middleware was used and the
workers were in the same local cluster.

Five computation precisions were used: $1e^{-1}$, $0.75e^{-1}$, $0.50e^{-1}$, $0.25e^{-1}$ and $1e^{-2}$.


\subsubsection{Results}
\label{sec:neurad_result}


In these experiments, we measured the same steps on both kinds of
executions. The steps consist of sending of local data and the
executable, the learning process, and retrieving the result. Table
\ref{tab:neurad_res} presents the execution times of the Neurad
application on 25 machines with XWCH (local and distributed deployment)
and without XWCH.


\begin{table}[h!]
  \centering
  \begin{tabular}[h!]{|c|c|c|c|c|}
    \hline
    Precision & 1 machine & Without XWCH & With XWCH & With local XWCH\\
    \hline
     $1e^{-1}$ & 5190 & 558 & 759 & 629\\
    $0.75e^{-1}$ & 6307 & 792 & 1298 & 801 \\
    $0.50e^{-1}$ & 7487 & 792 & 1010 & 844 \\
    $0.25e^{-1}$ & 7787 & 791 & 1000 & 852\\
    $1e^{-2}$ & 11030 & 1035 & 1447 & 1108 \\
    \hline
  \end{tabular}
\caption{Execution time in seconds of the Neurad application, with and without using the XWCH platform}
  \label{tab:neurad_res}
\end{table}

%\begin{table}[ht]
%  \centering
%  \begin{tabular}[h]{|c|c|c|}
%    \hline
%    Precision & Without XWCH & With XWCH \\
%    \hline
%    $1e^{-1}$ & $558$s & $759$s\\
%    \hline
%  \end{tabular}
%  \caption{Execution time in seconds of Neurad application, with and without using XtremWeb-CH platform}
%  \label{tab:neurad_res}
%\end{table}


These experiments show that the overhead induced by the use of the XWCH
platform is about $34\%$ in the distributed deployment and about $7\%$
in the local deployment. For this last one, the overhead is very acceptable regarding to the benefits of the platform.

Now, in the distributed deployment the overhead is also acceptable and can be explained by
different factors. First, we point out that the conditions of executions
are not really identical between with and without XWCH. For this last
one, though the same steps were done, all transfer processes are inside
a local cluster with a high bandwidth and a low latency. Whereas when
using XWCH, all transfer processes (between datawarehouses, workers, and
the coordinator) used a wide network area with a smaller bandwidth.

In addition, in executions without XWCH, all the machines started
immediately the computation, whereas when using the XWCH platform, a
latency is introduced by the fact that a task starts on a machine, only
when this one requests a task.

These experiments underline that deploying a local coordinator and one
or more warehouses near a cluster of workers can enhance computations
and platform performances. They also show a limited overhead due to the
use of the platform.


\end{document}



\section{Conclusion and future works}



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