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* New tree configuration of the project:

Browse source 
.../
   ...           + -- EO
   |             |
   |             |
   +-- src ----- + -- EDO
   |             |
   |             |
   +-- test      + -- MO
   |             |
   |             |
   +-- tutorial  + -- MOEO
   |             |
   |             |
   +-- doc       + -- SMP
   |             |
   |             |
   ...           + -- EOMPI
                 |
                 |
                 + -- EOSERIAL

Question for current maintainers: ./README: new release?

Also:

* Moving out eompi & eoserial modules (issue #2).

* Correction of the errors when executing "make doc" command.

* Adding a solution for the conflicting headers problem (see the two CMake Cache
 Values: PROJECT_TAG & PROJECT_HRS_INSTALL_SUBPATH) (issue #1)

* Header inclusions:
        ** src: changing absolute paths into relative paths ('#include <...>' -> '#include "..."')
        ** test, tutorial: changing relative paths into absolute paths ('#include "..."' -> '#include <...>')

* Moving out some scripts from EDO -> to the root

* Add a new script for compilation and installation (see build_gcc_linux_install)

* Compilation with uBLAS library or EDO module: now ok

* Minor modifications on README & INSTALL files

* Comment eompi failed tests with no end

*** TODO: CPack (debian (DEB) & RedHat (RPM) packages) (issues #6 & #7) ***
This commit is contained in:
Adèle Harrissart 2014-08-04 13:40:28 +02:00
commit 490e837f7a
2359 changed files with 7688 additions and 16329 deletions
Download patch file Download diff file Expand all files Collapse all files

272
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#ifndef _BASELESSON_H
#define _BASELESSON_H
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <vector>
#include <thread>
#include <chrono>
using namespace std;
int n = 10;
int** a;
int** b;
int bkv; //best known value
struct parameters
{
unsigned seed ;
int popSize;
int tSize;
string inst;
string loadName;
string schema;
double pCross;
double pMut;
int minGen;
int maxGen;
};
class Indi : public EO<eoMinimizingFitness> {
public:
int* solution;
int evalNb = 0;
Indi () {
solution = new int[n];
create();
}
Indi (const Indi & _problem){ // copy constructor
solution = new int[n];
for (int i = 0; i < n ; i++){
solution[i] = _problem.solution[i];
}
if (!_problem.invalid()) // if the solution has already been evaluated
fitness(_problem.fitness()); // copy the fitness
}
~Indi(){ // destructor
delete[] solution;
}
void operator= (const Indi & _problem){ // copy assignment operator
for (int i = 0; i < n ; i++){
solution[i] = _problem.solution[i];
}
fitness(_problem.fitness()); // copy the fitness
}
int& operator[] (unsigned i)
{
return solution[i];
}
void create(){ // create and initialize a solution
int random, temp;
for (int i=0; i< n; i++)
solution[i]=i;
// we want a random permutation so we shuffle
for (int i = 0; i < n; i++){
random = rand()%(n-i) + i;
temp = solution[i];
solution[i] = solution[random];
solution[random] = temp;
}
}
int evaluate() { // evaluate the solution
int cost=0;
for (int i=0; i<n; i++)
for (int j=0; j<n; j++)
cost += a[i][j] * b[solution[i]][solution[j]];
evalNb++;
//std::this_thread::sleep_for(std::chrono::milliseconds(1));
//std::cout << "Evaluation " << evalNb << std::endl;
return cost;
}
void printSolution() {
for (int i = 0; i < n ; i++)
std::cout << solution[i] << " " ;
std::cout << std::endl;
}
};
class IndiInit : public eoInit<Indi>
{
public:
void operator()(Indi & _problem)
{
_problem.create();
}
};
class IndiEvalFunc : public eoEvalFunc<Indi>
{
public:
void operator()(Indi & _problem)
{
_problem.fitness(_problem.evaluate());
}
};
class IndiXover : public eoQuadOp<Indi> {
public:
/* The two parameters in input are the parents.
The first parameter is also the output ie the child
*/
bool operator()(Indi & _problem1, Indi & _problem2)
{
int i;
int random, temp;
std::vector<int> unassigned_positions(n);
std::vector<int> remaining_items(n);
int j = 0;
/* 1) find the items assigned in different positions for the 2 parents */
for (i = 0 ; i < n ; i++){
if (_problem1.solution[i] != _problem2.solution[i]){
unassigned_positions[j] = i;
remaining_items[j] = _problem1.solution[i];
j++;
}
}
/* 2) shuffle the remaining items to ensure that remaining items
will be assigned at random positions */
for (i = 0; i < j; i++){
random = rand()%(j-i) + i;
temp = remaining_items[i];
remaining_items[i] = remaining_items[random];
remaining_items[random] = temp;
}
/* 3) copy the shuffled remaining items at unassigned positions */
for (i = 0; i < j ; i++)
_problem1.solution[unassigned_positions[i]] = remaining_items[i];
// crossover in our case is always possible
return true;
}
};
class IndiSwapMutation: public eoMonOp<Indi> {
public:
bool operator()(Indi& _problem) {
int i,j;
int temp;
// generate two different indices
i=rand()%n;
do
j = rand()%n;
while (i == j);
// swap
temp = _problem.solution[i];
_problem.solution[i] = _problem.solution[j];
_problem.solution[j] = temp;
return true;
}
};
void parseFile(eoParser & parser, parameters & param)
{
// For each parameter, you can in on single line
// define the parameter, read it through the parser, and assign it
param.seed = parser.createParam(unsigned(time(0)), "seed", "Random number seed", 'S').value(); // will be in default section General
// init and stop
param.loadName = parser.createParam(string(""), "Load","A save file to restart from",'L', "Persistence" ).value();
param.inst = parser.createParam(string(""), "inst","a dat file to read instances from",'i', "Persistence" ).value();
param.schema = parser.createParam(string(""), "schema","an xml file mapping process",'s', "Persistence" ).value();
param.popSize = parser.createParam(unsigned(10), "popSize", "Population size",'P', "Evolution engine" ).value();
param.tSize = parser.createParam(unsigned(2), "tSize", "Tournament size",'T', "Evolution Engine" ).value();
param.minGen = parser.createParam(unsigned(100), "minGen", "Minimum number of iterations",'g', "Stopping criterion" ).value();
param.maxGen = parser.createParam(unsigned(300), "maxGen", "Maximum number of iterations",'G', "Stopping criterion" ).value();
param.pCross = parser.createParam(double(0.6), "pCross", "Probability of Crossover", 'C', "Genetic Operators" ).value();
param.pMut = parser.createParam(double(0.1), "pMut", "Probability of Mutation", 'M', "Genetic Operators" ).value();
// the name of the "status" file where all actual parameter values will be saved
string str_status = parser.ProgramName() + ".status"; // default value
string statusName = parser.createParam(str_status, "status","Status file",'S', "Persistence" ).value();
// do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
// i.e. in case you need parameters somewhere else, postpone these
if (parser.userNeedsHelp())
{
parser.printHelp(cout);
exit(1);
}
if (statusName != "")
{
ofstream os(statusName.c_str());
os << parser; // and you can use that file as parameter file
}
}
void loadInstances(const char* filename, int& n, int& bkv, int** & a, int** & b)
{
ifstream data_file;
int i, j;
data_file.open(filename);
if (! data_file.is_open())
{
cout << "\n Error while reading the file " << filename << ". Please check if it exists !" << endl;
exit (1);
}
data_file >> n;
data_file >> bkv; // best known value
// ****************** dynamic memory allocation ****************** /
a = new int* [n];
b = new int* [n];
for (i = 0; i < n; i++)
{
a[i] = new int[n];
b[i] = new int[n];
}
// ************** read flows and distanceMatrixs matrices ************** /
for (i = 0; i < n; i++)
for (j = 0; j < n; j++)
data_file >> a[i][j];
for (i = 0; i < n; i++)
for (j = 0; j < n; j++)
data_file >> b[i][j];
data_file.close();
}
#endif

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tutorial/smp/CMakeLists.txt Executable file
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######################################################################################
### 0) Include lessons subdirectories
######################################################################################
add_subdirectory(Lesson1)
add_subdirectory(Lesson2)
add_subdirectory(Lesson3)
add_subdirectory(Lesson4)
######################################################################################
### 0) Install BaseFile for all lessons and data
######################################################################################
install(FILES BaseLesson.h DESTINATION ${PROJECT_HDRS_INSTALL_SUBPATH}/${PROJECT_TAG}/smp/tutorial COMPONENT tutorial)
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/lessonData.dat
${CMAKE_CURRENT_BINARY_DIR}/lessonData.dat)
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lessonData.dat DESTINATION share/${PROJECT_TAG}/smp/tutorial COMPONENT tutorial)

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tutorial/smp/Lesson1/CMakeLists.txt Executable file
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# Lesson 1
######################################################################################
### 0) Define files
######################################################################################
set(files
lesson1_eoEasyEA
)
######################################################################################
### 1) Create the lesson
######################################################################################
add_lesson(smp Lesson1 "${files}")
######################################################################################
### 2) Include dependencies
######################################################################################
#include_directories(${EO_SRC_DIR}/src
# ${SMP_SRC_DIR}/src
# ${PROBLEMS_SRC_DIR})
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/lesson1_data.dat
${CMAKE_CURRENT_BINARY_DIR}/lesson1_data.dat)

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tutorial/smp/Lesson1/QAP.h Executable file
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/*
<QAP.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 QAP_H
#define QAP_H
#include <paradiseo/eo.h>
/* global variables */
extern int n; // size
extern int** a; // matrix A
extern int** b; // matrix B
class Problem : public EO<eoMinimizingFitness> {
public:
int* solution;
Problem () {
solution = new int[n];
create();
}
Problem (const Problem & _problem){ // copy constructor
solution = new int[n];
for (int i = 0; i < n ; i++){
solution[i] = _problem.solution[i];
}
if (!_problem.invalid()) // if the solution has already been evaluated
fitness(_problem.fitness()); // copy the fitness
}
~Problem(){ // destructor
delete[] solution;
}
void operator= (const Problem & _problem){ // copy assignment operator
for (int i = 0; i < n ; i++){
solution[i] = _problem.solution[i];
}
fitness(_problem.fitness()); // copy the fitness
}
int& operator[] (unsigned i)
{
return solution[i];
}
void create(){ // create and initialize a solution
int random, temp;
for (int i=0; i< n; i++)
solution[i]=i;
// we want a random permutation so we shuffle
for (int i = 0; i < n; i++){
random = rand()%(n-i) + i;
temp = solution[i];
solution[i] = solution[random];
solution[random] = temp;
}
}
int evaluate() { // evaluate the solution
int cost=0;
for (int i=0; i<n; i++)
for (int j=0; j<n; j++)
cost += a[i][j] * b[solution[i]][solution[j]];
return cost;
}
void printSolution() {
for (int i = 0; i < n ; i++)
std::cout << solution[i] << " " ;
std::cout << std::endl;
}
};
#endif

121
tutorial/smp/Lesson1/QAPGA.h Executable file
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/*
<QAPGA.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 _QAPGA_h
#define _QAPGA_h
class ProblemInit : public eoInit<Problem>
{
public:
void operator()(Problem & _problem)
{
_problem.create();
}
};
class ProblemEvalFunc : public eoEvalFunc<Problem>
{
public:
void operator()(Problem & _problem)
{
_problem.fitness(_problem.evaluate());
}
};
class ProblemXover : public eoQuadOp<Problem> {
public:
/* The two parameters in input are the parents.
The first parameter is also the output ie the child
*/
bool operator()(Problem & _problem1, Problem & _problem2)
{
int i;
int random, temp;
int unassigned_positions[n];
int remaining_items[n];
int j = 0;
/* 1) find the items assigned in different positions for the 2 parents */
for (i = 0 ; i < n ; i++){
if (_problem1.solution[i] != _problem2.solution[i]){
unassigned_positions[j] = i;
remaining_items[j] = _problem1.solution[i];
j++;
}
}
/* 2) shuffle the remaining items to ensure that remaining items
will be assigned at random positions */
for (i = 0; i < j; i++){
random = rand()%(j-i) + i;
temp = remaining_items[i];
remaining_items[i] = remaining_items[random];
remaining_items[random] = temp;
}
/* 3) copy the shuffled remaining items at unassigned positions */
for (i = 0; i < j ; i++)
_problem1.solution[unassigned_positions[i]] = remaining_items[i];
// crossover in our case is always possible
return true;
}
};
class ProblemSwapMutation: public eoMonOp<Problem> {
public:
bool operator()(Problem& _problem) {
int i,j;
int temp;
// generate two different indices
i=rand()%n;
do
j = rand()%n;
while (i == j);
// swap
temp = _problem.solution[i];
_problem.solution[i] = _problem.solution[j];
_problem.solution[j] = temp;
return true;
}
};
#endif

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tutorial/smp/Lesson1/lesson1_data.dat Executable file
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12 224416
0 27 85 2 1 15 11 35 11 20 21 61
27 0 80 58 21 76 72 44 85 94 90 51
85 80 0 3 48 29 90 66 41 15 83 96
2 58 3 0 74 45 65 40 54 83 14 71
1 21 48 74 0 77 36 53 37 26 87 76
15 76 29 45 77 0 91 13 29 11 77 32
11 72 90 65 36 91 0 87 67 94 79 2
35 44 66 40 53 13 87 0 10 99 56 70
11 85 41 54 37 29 67 10 0 99 60 4
20 94 15 83 26 11 94 99 99 0 56 2
21 90 83 14 87 77 79 56 60 56 0 60
61 51 96 71 76 32 2 70 4 2 60 0
0 21 95 82 56 41 6 25 10 4 63 6
21 0 44 40 75 79 0 89 35 9 1 85
95 44 0 84 12 0 26 91 11 35 82 26
82 40 84 0 69 56 86 45 91 59 18 76
56 75 12 69 0 39 18 57 36 61 36 21
41 79 0 56 39 0 71 11 29 82 82 6
6 0 26 86 18 71 0 71 8 77 74 30
25 89 91 45 57 11 71 0 89 76 76 40
10 35 11 91 36 29 8 89 0 93 56 1
4 9 35 59 61 82 77 76 93 0 50 4
63 1 82 18 36 82 74 76 56 50 0 36
6 85 26 76 21 6 30 40 1 4 36 0

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tutorial/smp/Lesson1/lesson1_eoEasyEA.cpp Executable file
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/*
<lesson1_eoEasyEA.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
*/
/**
* Declaration of the necessary headers: In these are defined the class QAP,
* redefinition of the crossover, mutation, initialisation of solution.
*
*/
#include <paradiseo/smp.h>
#include "QAP.h"
#include "QAPGA.h"
#include <string>
using namespace std;
using namespace paradiseo::smp;
/** Set of parameters wrapped into a structure. We pass then the structure
* to a function which parses the parameters file. Doing so helps cleaning
* the code from the parts of reading the inputs.
*/
#include "parserStruct.h"
#include "utils.h"
/** The actual reading and parameters parsing is done inside this class utilities
*/
// Global variables
int n; // problem size
int** a;
int** b; // a and matrices
int bkv; //best known value
int main(int argc, char **argv)
{
if (argc < 2){
cout << "Please give a param file" << endl;
exit(1);
}
eoParser parser(argc, argv);
parameters param;
parseFile(parser, param);
rng.reseed(param.seed);
// Reading the a and b matrices of the QAP problem
loadInstances(param.inst.c_str(), n, bkv, a, b);
// Declaration of class wrapping the evaluation function of the QAP
ProblemEvalFunc plainEval;
eoEvalFuncCounter<Problem> eval(plainEval);
// Class involving a simple call to the function of initialisation of a solution
ProblemInit chromInit;
eoPop<Problem> pop(param.popSize, chromInit); // Initialise the population
// The robust tournament selection
eoDetTournamentSelect<Problem> selectOne(param.tSize);
// is now encapsulated in a eoSelectPerc (entage)
eoSelectPerc<Problem> select(selectOne);// by default rate==1
ProblemXover Xover; // CROSSOVER
ProblemSwapMutation mutationSwap; // MUTATION
// The operators are encapsulated into an eoTRansform object
eoSGATransform<Problem> transform(Xover, param.pCross, mutationSwap, param.pMut);
// REPLACE
eoPlusReplacement<Problem> replace;
eoGenContinue<Problem> genCont(param.maxGen); // generation continuation
try
{
// Create the algorithm
MWModel<eoEasyEA,Problem> mw(genCont, plainEval, select, transform, replace);
// Start a parallel evaluation on the population
mw.evaluate(pop);
std::cout << "Initial population :" << std::endl;
pop.sort();
std::cout << pop << std::endl;
// Start the algorithm on the population
mw(pop);
std::cout << "Final population :" << std::endl;
pop.sort();
std::cout << pop << std::endl;
}
catch(exception& e)
{
cout << "Exception: " << e.what() << '\n';
}
// desallocate memory
for (int i=0; i<n; i++){
delete[] a[i];
delete[] b[i];
}
delete[] a;
delete[] b;
return 1;
}

37
tutorial/smp/Lesson1/lesson1_eoEasyEA.param Executable file
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###### General ######
# --help=0 # -h : Prints this message
# --stopOnUnknownParam=1 # Stop if unkown param entered
# --seed=1104133126 # -S : Random number seed
###### Evolution Engine ######
--popSize=10 # -P : Population Size
--tSize=2 #tournament size
###### Output ######
# --useEval=1 # Use nb of eval. as counter (vs nb of gen.)
# --useTime=1 # Display time (s) every generation
# --printBestStat=1 # Print Best/avg/stdev every gen.
# --printPop=0 # Print sorted pop. every gen.
###### Output - Disk ######
# --resDir=Res # Directory to store DISK outputs
# --eraseDir=1 # erase files in dirName if any
# --fileBestStat=0 # Output bes/avg/std to file
###### Output - Graphical ######
# --plotBestStat=0 # Plot Best/avg Stat
# --plotHisto=0 # Plot histogram of fitnesses
###### Persistence ######
# --Load=L # -L : A save file to restart from
--inst=lesson1_data.dat # -i
--schema=schema.xml # -s
###### Stopping criterion ######
--maxGen=10 # -G : Maximum number of generations () = none)
--minGen=1 # -g : Minimum number of generations
###### Variation Operators ######
--pCross=0.7 # -C : Probability of Crossover
--pMut=0.8 # -M : Probability of Mutation

42
tutorial/smp/Lesson1/parserStruct.h Executable file
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/*
<parserStruct.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
*/
struct parameters
{
unsigned seed ;
int popSize;
int tSize;
string inst;
string loadName;
string schema;
double pCross;
double pMut;
int minGen;
int maxGen;
};

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tutorial/smp/Lesson1/utils.h Executable file
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/*
<utils.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 _UTILS_H
#define _UTILS_H
#include <stdlib.h>
#include <iostream>
#include <fstream>
using namespace std;
void parseFile(eoParser & parser, parameters & param)
{
// For each parameter, you can in on single line
// define the parameter, read it through the parser, and assign it
param.seed = parser.createParam(unsigned(time(0)), "seed", "Random number seed", 'S').value(); // will be in default section General
// init and stop
param.loadName = parser.createParam(string(""), "Load","A save file to restart from",'L', "Persistence" ).value();
param.inst = parser.createParam(string(""), "inst","a dat file to read instances from",'i', "Persistence" ).value();
param.schema = parser.createParam(string(""), "schema","an xml file mapping process",'s', "Persistence" ).value();
param.popSize = parser.createParam(unsigned(10), "popSize", "Population size",'P', "Evolution engine" ).value();
param.tSize = parser.createParam(unsigned(2), "tSize", "Tournament size",'T', "Evolution Engine" ).value();
param.minGen = parser.createParam(unsigned(100), "minGen", "Minimum number of iterations",'g', "Stopping criterion" ).value();
param.maxGen = parser.createParam(unsigned(300), "maxGen", "Maximum number of iterations",'G', "Stopping criterion" ).value();
param.pCross = parser.createParam(double(0.6), "pCross", "Probability of Crossover", 'C', "Genetic Operators" ).value();
param.pMut = parser.createParam(double(0.1), "pMut", "Probability of Mutation", 'M', "Genetic Operators" ).value();
// the name of the "status" file where all actual parameter values will be saved
string str_status = parser.ProgramName() + ".status"; // default value
string statusName = parser.createParam(str_status, "status","Status file",'S', "Persistence" ).value();
// do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
// i.e. in case you need parameters somewhere else, postpone these
if (parser.userNeedsHelp())
{
parser.printHelp(cout);
exit(1);
}
if (statusName != "")
{
ofstream os(statusName.c_str());
os << parser; // and you can use that file as parameter file
}
}
void loadInstances(const char* filename, int& n, int& bkv, int** & a, int** & b)
{
ifstream data_file;
int i, j;
data_file.open(filename);
if (! data_file.is_open())
{
cout << "\n Error while reading the file " << filename << ". Please check if it exists !" << endl;
exit (1);
}
data_file >> n;
data_file >> bkv; // best known value
// ****************** dynamic memory allocation ****************** /
a = new int* [n];
b = new int* [n];
for (i = 0; i < n; i++)
{
a[i] = new int[n];
b[i] = new int[n];
}
// ************** read flows and distanceMatrixs matrices ************** /
for (i = 0; i < n; i++)
for (j = 0; j < n; j++)
data_file >> a[i][j];
for (i = 0; i < n; i++)
for (j = 0; j < n; j++)
data_file >> b[i][j];
data_file.close();
}
#endif

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tutorial/smp/Lesson2/CMakeLists.txt Executable file
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# Lesson 2
######################################################################################
### 0) Define files
######################################################################################
set(files
lesson2_homogeneous
)
######################################################################################
### 1) Create the lesson
######################################################################################
add_lesson(smp Lesson2 "${files}")
######################################################################################
### 2) Include dependencies
######################################################################################
#include_directories(${EO_SRC_DIR}/src
# ${SMP_SRC_DIR}/src
# ${PROBLEMS_SRC_DIR})

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tutorial/smp/Lesson2/lesson2_homogeneous.cpp Executable file
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/*
<lesson2_homogeneous.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
*/
/*///////////////////////////////////////////////////////////////////
// SMP Tutorial 2 : Homogeneous Model
// This file shows how to create an homogeneous
// island model with 3 islands, a complete topology
// and different parameters for each island.
/*///////////////////////////////////////////////////////////////////
#include <paradiseo/smp.h>
#include <paradiseo/eo.h>
#include "../BaseLesson.h"
using namespace paradiseo::smp;
using namespace std;
int main(void)
{
// Defining parameters
typedef struct {
unsigned popSize = 1000;
unsigned tSize = 2;
double pCross = 0.8;
double pMut = 0.7;
unsigned maxGen = 1000;
} Param;
Param param;
// Fixing the seed
rng.reseed(42);
// Load instance
loadInstances("../lessonData.dat", n, bkv, a, b);
//Common part to all islands
IndiEvalFunc plainEval;
IndiInit chromInit;
eoDetTournamentSelect<Indi> selectOne(param.tSize);
eoSelectPerc<Indi> select(selectOne);// by default rate==1
IndiXover Xover; // CROSSOVER
IndiSwapMutation mutationSwap; // MUTATION
eoSGATransform<Indi> transform(Xover, param.pCross, mutationSwap, param.pMut);
eoPlusReplacement<Indi> replace;
// MODEL
// Topologies
Topology<Complete> topo;
IslandModel<Indi> model(topo);
// ISLAND 1
// // Algorithm part
eoGenContinue<Indi> genCont(param.maxGen+100);
eoPop<Indi> pop(param.popSize, chromInit);
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi> criteria(5);
eoDetTournamentSelect<Indi> selectOne1(20);
eoSelectNumber<Indi> who(selectOne1, 3);
MigPolicy<Indi> migPolicy;
migPolicy.push_back(PolicyElement<Indi>(who, criteria));
// // Integration policy
eoPlusReplacement<Indi> intPolicy;
Island<eoEasyEA,Indi> test(pop, intPolicy, migPolicy, genCont, plainEval, select, transform, replace);
// ISLAND 1
// // Algorithm part
eoGenContinue<Indi> genCont_2(param.maxGen); // generation continuation
eoPop<Indi> pop2(30, chromInit);
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi> criteria_2(5);
eoDetTournamentSelect<Indi> selectOne_2(25);
eoSelectNumber<Indi> who_2(selectOne_2, 5);
MigPolicy<Indi> migPolicy_2;
migPolicy_2.push_back(PolicyElement<Indi>(who_2, criteria_2));
// // Integration policy
eoPlusReplacement<Indi> intPolicy_2;
Island<eoEasyEA,Indi> test2(pop2, intPolicy_2, migPolicy_2, genCont_2, plainEval, select, transform, replace);
// Island 3
// // Algorithm part
eoGenContinue<Indi> genCont_3(param.maxGen);
eoPop<Indi> pop3(30, chromInit);
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi> criteria_3(10);
eoDetTournamentSelect<Indi> selectOne_3(15);
eoSelectNumber<Indi> who_3(selectOne_3, 1);
MigPolicy<Indi> migPolicy_3;
migPolicy.push_back(PolicyElement<Indi>(who_3, criteria_3));
// // Integration policy
eoPlusReplacement<Indi> intPolicy_3;
Island<eoEasyEA,Indi> test3(pop3, intPolicy_3, migPolicy_3, genCont_3, plainEval, select, transform, replace);
try
{
model.add(test);
model.add(test2);
model.add(test3);
model();
cout << test.getPop() << endl;
cout << test2.getPop() << endl;
cout << test3.getPop() << endl;
}
catch(exception& e)
{
cout << "Exception: " << e.what() << '\n';
}
return 0;
}

23
tutorial/smp/Lesson3/CMakeLists.txt Executable file
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# Lesson 3
######################################################################################
### 0) Define files
######################################################################################
set(files
lesson3_heterogeneous
)
######################################################################################
### 1) Create the lesson
######################################################################################
add_lesson(smp Lesson3 "${files}")
######################################################################################
### 2) Include dependencies
######################################################################################
#include_directories(${EO_SRC_DIR}/src
# ${SMP_SRC_DIR}/src
# ${PROBLEMS_SRC_DIR})

226
tutorial/smp/Lesson3/lesson3_heterogeneous.cpp Executable file
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/*
<lesson3_heterogeneous.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
*/
/*///////////////////////////////////////////////////////////////////
// SMP Tutorial 3 : Heterogeneous Model
// This file shows how to create an heterogeneous
// island model with 2 islands : an eoEasyEA island and a PSO.
// The file can be broken down into 3 parts :
// The PSO part, with algorithm parameters and PSO Island creatation.
// Then, the eoEasyEA part.
// And finally, the model creation.
// On top of that, you conversion functions are defined at the
// begining of this file.
/*///////////////////////////////////////////////////////////////////
#include <paradiseo/smp.h>
#include <paradiseo/eo.h>
#include <paradiseo/eo/ga.h>
#include "../BaseLesson.h"
using namespace paradiseo::smp;
using namespace std;
typedef eoBit<double> Indi2; // A bitstring with fitness double
// Conversion functions
Indi2 fromBase(Indi& i, unsigned size)
{
(void)i;
// Dummy conversion. We just create a new Indi2
Indi2 v;
for (unsigned ivar=0; ivar<size; ivar++)
{
bool r = rng.flip(); // new value, random in {0,1}
v.push_back(r); // append that random value to v
}
std::cout << "Convert from base : " << v << std::endl;
return v;
}
Indi toBase(Indi2& i)
{
(void)i;
// Dummy conversion. We just create a new Indi
Indi v;
std::cout << "Convert to base : " << v << std::endl;
return v;
}
// Eval function for the PSO
// A simple fitness function that computes the number of ones of a bitstring
// @param _Indi2 A biststring Indi2vidual
double binary_value(const Indi2 & _Indi2)
{
double sum = 0;
for (unsigned i = 0; i < _Indi2.size(); i++)
sum += _Indi2[i];
return sum;
}
int main(void)
{
//////////////////////////////////////////////////////////////////
// PSO PART
//////////////////////////////////////////////////////////////////
// PSO general parameters
const unsigned int SEED = 42; // seed for random number generator
const unsigned int T_SIZE = 3; // size for tournament selection
const unsigned int VEC_SIZE = 16; // Number of bits in genotypes
const unsigned int POP_SIZE = 10; // Size of population
const unsigned int MAX_GEN = 10; // Maximum number of generation before STOP
const float CROSS_RATE = 0.8; // Crossover rate
const double P_MUT_PER_BIT = 0.01; // probability of bit-flip mutation
const float MUT_RATE = 1.0; // mutation rate
rng.reseed(SEED);
eoEvalFuncPtr<Indi2> eval(binary_value);
// PSO population initialization
eoPop<Indi2> pop;
for(unsigned int igeno=0; igeno<POP_SIZE; igeno++)
{
Indi2 v; // void Indi2vidual, to be filled
for (unsigned ivar=0; ivar<VEC_SIZE; ivar++)
{
bool r = rng.flip(); // new value, random in {0,1}
v.push_back(r); // append that random value to v
}
eval(v); // evaluate it
pop.push_back(v); // and put it in the population
}
// ISLAND 1 : PSO
// // Algorithm part
eoDetTournamentSelect<Indi2> select(T_SIZE); // T_SIZE in [2,POP_SIZE]
eo1PtBitXover<Indi2> xover;
eoBitMutation<Indi2> mutation(P_MUT_PER_BIT);
eoGenContinue<Indi2> continuator(MAX_GEN);
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi2> criteria(1);
eoDetTournamentSelect<Indi2> selectOne(2);
eoSelectNumber<Indi2> who(selectOne, 1);
MigPolicy<Indi2> migPolicy;
migPolicy.push_back(PolicyElement<Indi2>(who, criteria));
// // Integration policy
eoPlusReplacement<Indi2> intPolicy;
// We bind conversion functions
auto frombase = std::bind(fromBase, std::placeholders::_1, VEC_SIZE);
auto tobase = std::bind(toBase, std::placeholders::_1);
Island<eoSGA,Indi2, Indi> gga(frombase, tobase, pop, intPolicy, migPolicy, select, xover, CROSS_RATE, mutation, MUT_RATE, eval, continuator);
//////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////
// EasyEA PART
//////////////////////////////////////////////////////////////////
// EA general parameters
typedef struct {
unsigned popSize = 10;
unsigned tSize = 2;
double pCross = 0.8;
double pMut = 0.7;
unsigned maxGen = 10;
} Param;
Param param;
loadInstances("../lessonData.dat", n, bkv, a, b);
// Evaluation function
IndiEvalFunc plainEval;
// Init a solution
IndiInit chromInit;
// Define selection
eoDetTournamentSelect<Indi> selectOne2(param.tSize);
eoSelectPerc<Indi> select2(selectOne2);// by default rate==1
// Define operators for crossover and mutation
IndiXover Xover; // CROSSOVER
IndiSwapMutation mutationSwap; // MUTATION
// Encapsule in a tranform operator
eoSGATransform<Indi> transform(Xover, param.pCross, mutationSwap, param.pMut);
// Define replace operator
eoPlusReplacement<Indi> replace;
eoGenContinue<Indi> genCont(param.maxGen); // generation continuation
eoPop<Indi> pop2(param.popSize, chromInit);
// ISLAND 2 : EasyEA
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi> criteria2(1);
eoDetTournamentSelect<Indi> selectOne3(5);
eoSelectNumber<Indi> who2(selectOne3, 2);
MigPolicy<Indi> migPolicy2;
migPolicy2.push_back(PolicyElement<Indi>(who2, criteria2));
// // Integration policy
eoPlusReplacement<Indi> intPolicy2;
Island<eoEasyEA,Indi> test(pop2, intPolicy2, migPolicy2, genCont, plainEval, select2, transform, replace);
//////////////////////////////////////////////////////////////////
// MODEL CREATION
Topology<Complete> topo;
IslandModel<Indi> model(topo);
try
{
model.add(test);
model.add(gga);
model();
cout << test.getPop() << endl;
cout << gga.getPop() << endl;
}
catch(exception& e)
{
cout << "Exception: " << e.what() << '\n';
}
return 0;
}

23
tutorial/smp/Lesson4/CMakeLists.txt Executable file
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# Lesson 4
######################################################################################
### 0) Define files
######################################################################################
set(files
lesson4_topology
)
######################################################################################
### 1) Create the lesson
######################################################################################
add_lesson(smp Lesson4 "${files}")
######################################################################################
### 2) Include dependencies
######################################################################################
#include_directories(${EO_SRC_DIR}/src
# ${SMP_SRC_DIR}/src
# ${PROBLEMS_SRC_DIR})

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tutorial/smp/Lesson4/lesson4_topology.cpp Executable file
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/*
<lesson4_topology.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
*/
/*///////////////////////////////////////////////////////////////////
// SMP Tutorial 4 : Advanced Island Model Mecanisms
// This file shows how to create events called by islands.
// In our case, we would like to change the topology after 10 seconds
// of computation.
/*///////////////////////////////////////////////////////////////////
#include <paradiseo/smp.h>
#include <paradiseo/eo.h>
#include <chrono>
#include "../BaseLesson.h"
using namespace paradiseo::smp;
using namespace std;
/*
Simple function to change topology of a given model, once, after 10 seconds.
*/
void changeTopo(IslandModel<Indi>* _model, AbstractTopology& _topo)
{
static auto start = std::chrono::system_clock::now();
auto now = std::chrono::system_clock::now();
auto elapsed = now - start;
static bool first = false;
if(std::chrono::duration_cast<std::chrono::milliseconds>(elapsed).count() > 10000 && !first)
{
std::cout << "Changing topology !" << std::endl;
_model->setTopology(_topo);
first = true;
}
}
int main(void)
{
// Defining parameters
typedef struct {
unsigned popSize = 1000;
unsigned tSize = 2;
double pCross = 0.8;
double pMut = 0.7;
unsigned maxGen = 1000;
} Param;
Param param;
// Load instance
loadInstances("../lessonData.dat", n, bkv, a, b);
//Common part to all islands
IndiEvalFunc plainEval;
IndiInit chromInit;
eoDetTournamentSelect<Indi> selectOne(param.tSize);
eoSelectPerc<Indi> select(selectOne);// by default rate==1
IndiXover Xover; // CROSSOVER
IndiSwapMutation mutationSwap; // MUTATION
eoSGATransform<Indi> transform(Xover, param.pCross, mutationSwap, param.pMut);
eoPlusReplacement<Indi> replace;
// MODEL
// Topologies
Topology<Complete> topo;
IslandModel<Indi> model(topo);
// ISLAND 1
// // Algorithm part
eoGenContinue<Indi> genCont(param.maxGen+100);
eoPop<Indi> pop(param.popSize, chromInit);
// // Emigration policy
// // // Element 1
eoPeriodicContinue<Indi> criteria(5);
eoDetTournamentSelect<Indi> selectOne1(20);
eoSelectNumber<Indi> who(selectOne1, 3);
Topology<Ring> topo2;
/*
We need to bind our function in a std::function object.
Then, we create a Notifier that we add to our island thanks
to an eoCheckPoint.
*/
auto task = std::bind(changeTopo, &model, topo2);
Notifier topoChanger(task);
eoCheckPoint<Indi> ck(genCont);
ck.add(topoChanger);
MigPolicy<Indi> migPolicy;
migPolicy.push_back(PolicyElement<Indi>(who, criteria));
// // Integration policy
eoPlusReplacement<Indi> intPolicy;
Island<eoEasyEA,Indi> test(pop, intPolicy, migPolicy, ck, plainEval, select, transform, replace);
try
{
model.add(test);
// The topology will change after 10 seconds of computation
model();
}
catch(exception& e)
{
cout << "Exception: " << e.what() << '\n';
}
return 0;
}

27
tutorial/smp/lessonData.dat Executable file
View file

@ -0,0 +1,27 @@
12 224416
0 27 85 2 1 15 11 35 11 20 21 61
27 0 80 58 21 76 72 44 85 94 90 51
85 80 0 3 48 29 90 66 41 15 83 96
2 58 3 0 74 45 65 40 54 83 14 71
1 21 48 74 0 77 36 53 37 26 87 76
15 76 29 45 77 0 91 13 29 11 77 32
11 72 90 65 36 91 0 87 67 94 79 2
35 44 66 40 53 13 87 0 10 99 56 70
11 85 41 54 37 29 67 10 0 99 60 4
20 94 15 83 26 11 94 99 99 0 56 2
21 90 83 14 87 77 79 56 60 56 0 60
61 51 96 71 76 32 2 70 4 2 60 0
0 21 95 82 56 41 6 25 10 4 63 6
21 0 44 40 75 79 0 89 35 9 1 85
95 44 0 84 12 0 26 91 11 35 82 26
82 40 84 0 69 56 86 45 91 59 18 76
56 75 12 69 0 39 18 57 36 61 36 21
41 79 0 56 39 0 71 11 29 82 82 6
6 0 26 86 18 71 0 71 8 77 74 30
25 89 91 45 57 11 71 0 89 76 76 40
10 35 11 91 36 29 8 89 0 93 56 1
4 9 35 59 61 82 77 76 93 0 50 4
63 1 82 18 36 82 74 76 56 50 0 36
6 85 26 76 21 6 30 40 1 4 36 0