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adding custom topologies, src and test

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lasnier 2013-01-11 00:20:09 +01:00
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2
smp/src/CMakeLists.txt
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@ -28,6 +28,8 @@ set (SMP_FILE
topology/ring.cpp
topology/hypercubic.cpp
topology/mesh.cpp
topology/customBooleanTopology.cpp
topology/customStochasticTopology.cpp
notifier.cpp
islandModelWrapper.h
)

3
smp/src/smp.h
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@ -49,5 +49,8 @@ Contact: paradiseo-help@lists.gforge.inria.fr
#include <topology/star.h>
#include <topology/hypercubic.h>
#include <topology/mesh.cpp>
#include <topology/customBooleanTopology.h>
#include <topology/customBooleanTopology.h>
#endif

119
smp/src/topology/customBooleanTopology.cpp Normal file
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@ -0,0 +1,119 @@
/*
<customBooleanTopology.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2012
Alexandre Quemy, Thibault Lasnier - INSA Rouen
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <topology/customBooleanTopology.h>
#include <vector>
#include <assert.h>
#include <string>
#include <fstream>
#include <sstream>
#include <stdexcept>
#include <iostream>
paradiseo::smp::CustomBooleanTopology::CustomBooleanTopology(std::string filename)
{
std :: ifstream f(filename);
if (f)
{
int temp;
unsigned size;
bool isNeighbor, isFirst = true;
std::string line;
std::vector<bool> lineVector;
while(getline(f, line))
{
lineVector.clear();
//line contains a line of text from the file
std::istringstream tokenizer(line);
std::string token;
while(tokenizer>> temp >> std::skipws)
{
//white spaces are skipped, and the integer is converted to boolean, to be stored
isNeighbor = (bool) temp;
lineVector.push_back(isNeighbor);
}
//if this is the first line, we must initiate the variable size
if(isFirst)
{
size = lineVector.size();
isFirst=false;
}
//for each vector non empty, if the size is not equal to the others, error
if(lineVector.size() != size && !lineVector.empty())
throw std::runtime_error("Mistake in the topology, line "+ std::to_string(_matrix.size()+1) );
if(!lineVector.empty())
_matrix.push_back(lineVector);
}
//for each vector, verify if the size is equal to the size of the final matrix
for(auto& line : _matrix)
if(line.size() != _matrix.size())
throw std::runtime_error("Mistake in the topology, matrix is not square" );
f.close () ;
}
else
{
throw std::runtime_error("Error occured while reading the topology file " + filename);
}
}
std::vector<unsigned> paradiseo::smp::CustomBooleanTopology::getIdNeighbors(unsigned idNode) const
{
std::vector<unsigned> neighbors;
for(unsigned j=0; j<_matrix.size();j++)
if(_matrix[idNode][j])
neighbors.push_back(j);
return neighbors;
}
void paradiseo::smp::CustomBooleanTopology::construct(unsigned nbNode)
{
assert(nbNode==_matrix.size());
}
void paradiseo::smp::CustomBooleanTopology::isolateNode(unsigned idNode)
{
for(int i=0;i<_matrix.size();i++)
{
//Line of idNode to false : no connection FROM this node
_matrix[idNode][i]=false;
//Column of idNode to false : no connection TO this node
_matrix[i][idNode]=false;
}
}

77
smp/src/topology/customBooleanTopology.h Normal file
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@ -0,0 +1,77 @@
/*
<customBooleanTopology.h>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2012
Alexandre Quemy, Thibault Lasnier - INSA Rouen
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#ifndef CUST_BOOL_TOPO_H_
#define CUST_BOOL_TOPO_H_
#include <vector>
#include <topology/abstractTopology.h>
#include <string>
namespace paradiseo
{
namespace smp
{
class CustomBooleanTopology : public AbstractTopology
{
public :
/**
*Constructor for a custom topology from a file
*@param filename Name of the file, must be in the same directory as the executable
*/
CustomBooleanTopology(std::string filename);
/**
* Inherited from AbstractTopology
* @see smp::topology::AbstractTopology::getIdNeighbors
*/
std::vector<unsigned> getIdNeighbors(unsigned idNode) const;
/**
* Inherited from AbstractTopology : a custom topology cannot be reconstructed in a different way, so the method throws an error if nbNode doesn't match with the actual number of nodes.
* @param nbNode number of nodes for the topology
*/
void construct(unsigned nbNode);
/**
*Inherited from AbstractTopology : changes the topology : removes any connection from/to the given node.
*@param idNode index of the node to be isolated
*/
void isolateNode(unsigned idNode);
private :
std::vector<std::vector<bool>> _matrix;
};
}
}
#endif

129
smp/src/topology/customStochasticTopology.cpp Normal file
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@ -0,0 +1,129 @@
/*
<customStochasticTopology.cpp>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2012
Alexandre Quemy, Thibault Lasnier - INSA Rouen
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#include <topology/customStochasticTopology.h>
#include <vector>
#include <assert.h>
#include <string>
#include <random>
#include <fstream>
#include <sstream>
#include <stdexcept>
#include <iostream>
paradiseo::smp::CustomStochasticTopology::CustomStochasticTopology(std::string filename)
{
std :: ifstream f(filename);
if (f)
{
double temp;
unsigned size;
double isNeighbor, isFirst = true;
std::string line;
std::vector<double> lineVector;
while(getline(f, line))
{
lineVector.clear();
//line contains a line of text from the file
std::istringstream tokenizer(line);
std::string token;
while(tokenizer>> temp >> std::skipws)
{
//white spaces are skipped, and the integer is converted to boolean, to be stored
if(temp<0)
isNeighbor = 0;
else if(temp>1)
isNeighbor = 1;
else
isNeighbor = (double) temp;
lineVector.push_back(isNeighbor);
}
//if this is the first line, we must initiate the variable size
if(isFirst)
{
size = lineVector.size();
isFirst=false;
}
//for each vector non empty, if the size is not equal to the others, error
if(lineVector.size() != size && !lineVector.empty())
throw std::runtime_error("Mistake in the topology, line "+ std::to_string(_matrix.size()+1) );
if(!lineVector.empty())
_matrix.push_back(lineVector);
}
//for each vector, verify if the size is equal to the size of the final matrix
for(auto& line : _matrix)
if(line.size() != _matrix.size())
throw std::runtime_error("Mistake in the topology, matrix is not square" );
f.close () ;
}
else
{
throw std::runtime_error("Error occured while reading the topology file " + filename);
}
}
std::vector<unsigned> paradiseo::smp::CustomStochasticTopology::getIdNeighbors(unsigned idNode) const
{
std::random_device rd;
std::mt19937 gen(rd());
std::uniform_real_distribution<> dis(0,1);
std::vector<unsigned> neighbors;
for(unsigned j=0; j<_matrix.size();j++)
if(_matrix[idNode][j] > dis(gen))
neighbors.push_back(j);
return neighbors;
}
void paradiseo::smp::CustomStochasticTopology::construct(unsigned nbNode)
{
assert(nbNode==_matrix.size());
}
void paradiseo::smp::CustomStochasticTopology::isolateNode(unsigned idNode)
{
for(int i=0;i<_matrix.size();i++)
{
//Line of idNode to false : no connection FROM this node
_matrix[idNode][i]=0;
//Column of idNode to false : no connection TO this node
_matrix[i][idNode]=0;
}
}

78
smp/src/topology/customStochasticTopology.h Normal file
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@ -0,0 +1,78 @@
/*
<customStochasticTopology.h>
Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2012
Alexandre Quemy, Thibault Lasnier - INSA Rouen
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can ue,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
ParadisEO WebSite : http://paradiseo.gforge.inria.fr
Contact: paradiseo-help@lists.gforge.inria.fr
*/
#ifndef CUST_STOCH_TOPO_H_
#define CUST_STOCH_TOPO_H_
#include <vector>
#include <topology/abstractTopology.h>
#include <string>
namespace paradiseo
{
namespace smp
{
class CustomStochasticTopology : public AbstractTopology
{
public :
/**
*Constructor for a custom topology from a file
*@param filename Name of the file, must be in the same directory as the executable
*/
CustomStochasticTopology(std::string filename);
/**
* Inherited from AbstractTopology
* @see smp::topology::AbstractTopology::getIdNeighbors
*/
std::vector<unsigned> getIdNeighbors(unsigned idNode) const;
/**
* Inherited from AbstractTopology : a custom topology cannot be reconstructed in a different way, so the method throws an error if nbNode doesn't match with the actual number of nodes.
* @param nbNode number of nodes for the topology
*/
void construct(unsigned nbNode);
/**
*Inherited from AbstractTopology : changes the topology : removes any connection from/to the given node.
*@param idNode index of the node to be isolated
*/
void isolateNode(unsigned idNode);
private :
std::vector<std::vector<double>> _matrix;
};
}
}
#endif

13
smp/test/CMakeLists.txt
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@ -20,6 +20,7 @@ set (TEST_LIST
t-smpMI_Homogeneous
t-smpMI_Heterogeneous
t-smpMI_Wrapper
t-smpCustomTopo
)
######################################################################################
@ -39,3 +40,15 @@ execute_process(
${CMAKE_CURRENT_SOURCE_DIR}/t-data.dat
${CMAKE_CURRENT_BINARY_DIR}/t-data.dat)
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/t-data.dat DESTINATION share${INSTALL_SUB_DIR}/smp/test COMPONENT tests)
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/data-topo-bool
${CMAKE_CURRENT_BINARY_DIR}/data-topo-bool)
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/data-topo-bool DESTINATION share${INSTALL_SUB_DIR}/smp/test COMPONENT tests)
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/data-topo-stoch
${CMAKE_CURRENT_BINARY_DIR}/data-topo-stoch)
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/data-topo-stoch DESTINATION share${INSTALL_SUB_DIR}/smp/test COMPONENT tests)

4
smp/test/data-topo-bool Normal file
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@ -0,0 +1,4 @@
0 1 0 0
1 0 1 1
0 1 0 1
1 0 1 0

3
smp/test/data-topo-stoch Normal file
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@ -0,0 +1,3 @@
.25 .5 .75
.2 .1 .05
.9 .2 .03

118
smp/test/t-smpCustomTopo.cpp Normal file
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@ -0,0 +1,118 @@
#include <topology/customBooleanTopology.h>
#include <topology/customStochasticTopology.h>
#include <iostream>
#include <sstream>
#include <fstream>
#include <vector>
#include <assert.h>
#include <cmath>
using namespace paradiseo::smp;
int main()
{
std::vector<unsigned> value;
//TEST OF CUSTOM BOOLEAN TOPOLOGY
CustomBooleanTopology topo_bool("data-topo-bool");
std::vector<unsigned> neighbors = topo_bool.getIdNeighbors(0);
value.clear();
value.push_back(1);
assert(neighbors == value);
///////////////////////////////////////////////////////
neighbors = topo_bool.getIdNeighbors(1);
value.clear();
value.push_back(0);
value.push_back(2);
value.push_back(3);
assert(neighbors == value);
//////////////////////////////////////////////////////
neighbors = topo_bool.getIdNeighbors(2);
value.clear();
value.push_back(1);
value.push_back(3);
assert(neighbors == value);
//////////////////////////////////////////////////////
neighbors = topo_bool.getIdNeighbors(3);
value.clear();
value.push_back(0);
value.push_back(2);
assert(neighbors == value);
//TEST OF CUSTOM STOCHASTIC TOPOLOGY
CustomStochasticTopology topo_stoch("data-topo-stoch");
std::vector<std::vector<double>> matrix;
matrix.resize(3);
for(auto& line : matrix)
line.resize(3);
//Computation of the mean probability
int it_nb = 1000;
for(int i = 0 ; i < it_nb ; i++)
{
for(int j = 0; j < 3; j++)
{
neighbors = topo_stoch.getIdNeighbors(j);
for(auto& node : neighbors)
{
matrix[j][node]++;
}
}
}
for(auto& line : matrix)
{
for(auto& edge : line)
edge = edge/it_nb;
}
//Reading the actual matrix
std :: ifstream f("data-topo-stoch");
std::vector<std::vector<double>> _matrix;
if (f)
{
double temp;
unsigned size;
double isNeighbor, isFirst = true;
std::string line;
std::vector<double> lineVector;
while(getline(f, line))
{
lineVector.clear();
//line contains a line of text from the file
std::istringstream tokenizer(line);
std::string token;
while(tokenizer>> temp >> std::skipws)
{
//white spaces are skipped, and the integer is converted to boolean, to be stored
if(temp<0)
isNeighbor = 0;
else if(temp>1)
isNeighbor = 1;
else
isNeighbor = (double) temp;
lineVector.push_back(isNeighbor);
}
if(!lineVector.empty())
_matrix.push_back(lineVector);
}
f.close () ;
}
//Comparison to the actual matrix : _matrix
for(int i = 0; i < matrix.size(); i++)
for(int j = 0; j < matrix.size(); j++)
assert(std::abs(_matrix[i][j] - matrix[i][j]) < .05);
}

1
smp/test/t-smpTopo.cpp
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@ -1,6 +1,7 @@
#include <smp>
#include <iostream>
#include <vector>
#include <assert.h>
using namespace paradiseo::smp;