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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
65 changed files with 7688 additions and 16329 deletions
Download patch file Download diff file Expand all files Collapse all files

116
test/eo/CMakeLists.txt Executable file
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###############################################################################
##
## CMakeLists file for eo/test
##
###############################################################################
######################################################################################
### 1) Include the sources
######################################################################################
#include_directories(${EO_SRC_DIR}/src)
#include_directories(${EO_SRC_DIR}/contrib)
include_directories(${EO_SRC_DIR}/contrib/MGE)
#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
######################################################################################
### 2) Specify where CMake can find the libraries
######################################################################################
#link_directories(${EO_BIN_DIR}/lib)
######################################################################################
### 3) Define your targets and link the librairies
######################################################################################
set (TEST_LIST
t-eofitness
t-eoRandom
t-eobin
t-eoVirus
t-MGE
t-MGE1bit
t-MGE-control
t-eoStateAndParser
t-eoCheckpointing
t-eoSSGA
t-eoExternalEO
t-eoSymreg
t-eo
t-eoReplacement
t-eoSelect
t-eoGenOp
t-eoGA
t-eoReal
t-eoVector
t-eoESAll
t-eoPBIL
t-eoFitnessAssembled
t-eoFitnessAssembledEA
t-eoRoulette
t-eoSharing
t-eoCMAES
t-eoSecondsElapsedContinue
t-eoRNG
t-eoEasyPSO
t-eoInt
t-eoInitPermutation
t-eoSwapMutation
t-eoShiftMutation
t-eoTwoOptMutation
t-eoRingTopology
t-eoSyncEasyPSO
t-eoOrderXover
t-eoExtendedVelocity
t-eoLogger
#t-eoIQRStat # Temporary by-passed in order to test coverage
t-eoParallel
#t-openmp # does not work anymore since functions used in this test were removed from EO
#t-eoDualFitness
t-eoParser
)
foreach (test ${TEST_LIST})
set ("T_${test}_SOURCES" "${test}.cpp")
endforeach (test)
if(ENABLE_MINIMAL_CMAKE_TESTING)
set (MIN_TEST_LIST t-eoEasyPSO)
foreach (mintest ${MIN_TEST_LIST})
set ("T_${mintest}_SOURCES" "${mintest}.cpp")
add_executable(${mintest} ${T_${mintest}_SOURCES})
add_test(${mintest} ${mintest})
target_link_libraries(${mintest} ga es cma eoutils eo)
endforeach (mintest)
elseif(ENABLE_CMAKE_TESTING)
foreach (test ${TEST_LIST})
add_executable(${test} ${T_${test}_SOURCES})
add_test(${test} ${test})
target_link_libraries(${test} ga es cma eoutils eo)
install(TARGETS ${test} RUNTIME DESTINATION share/${PROJECT_TAG}/eo/test COMPONENT test)
endforeach (test)
set(RESOURCES
boxplot.py
boxplot_to_png.py
boxplot_to_pdf.py
t-openmp.py
)
foreach(file ${RESOURCES})
execute_process(
COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_SOURCE_DIR}/${file}
${CMAKE_CURRENT_BINARY_DIR}/${file}
)
endforeach(file)
endif(ENABLE_MINIMAL_CMAKE_TESTING)
######################################################################################

7
test/eo/CTestConfig.cmake Executable file
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set(CTEST_PROJECT_NAME "ParadisEO")
set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "cdash.inria.fr")
set(CTEST_DROP_LOCATION "/CDash/submit.php?project=ParadisEO")
set(CTEST_DROP_SITE_CDASH TRUE)

36
test/eo/ChangeLog Executable file
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2006-12-04 Jochen Kpper <jochen@fhi-berlin.mpg.de>
* Makefile.am: Add t-eoRNG
* t-eoRNG.cpp: Start test for random number generator.
2006-12-02 Jochen Kpper <jochen@fhi-berlin.mpg.de>
* t-MGE1bit.cpp: Change float to double.
* t-eoGenOp.cpp (init): Do not add std::ends to end of string, as this
results in escape-codes (^@) to be printed at runtime and is not
necessary anyway.
* test/t-eoSymreg.cpp (SymregNode::operator()): Initialize r1 and r2 to
avoid compiler warnings.
2006-07-02 Thomas Legrand <thomas.legrand@inria.fr>
* test/t-eoEasyPSO.cpp: added PSO test
* test/Makefile.am: added PSO test
2006-02-27 Thomas Legrand <thomas.legrand@inria.fr>
* test/t-eoSyncEasyPSO.cpp: added synchronous PSO test
* test/t-eoEasyPSO.cpp: customized PSO test (initialization)
* test/Makefile.am: added synchronous PSO test
* Local Variables:
* coding: iso-8859-1
* mode: flyspell
* fill-column: 80
* End:

502
test/eo/LICENSE Executable file
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@ -0,0 +1,502 @@
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You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the library, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!

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/*
RoyalRoad.h
-- Implementation of the Royal Road function for any length and block size
(c) GeNeura Team 2001, Marc Schoenauer 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
CVS Info: $Date: 2001-06-21 12:03:17 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/test/RoyalRoad.h,v 1.3 2001-06-21 12:03:17 jmerelo Exp $ $Author: jmerelo $
*/
#ifndef RoyalRoad_h
#define RoyalRoad_h
#include <paradiseo/eo.h>
template<class EOT>
class RoyalRoad: public eoEvalFunc<EOT> {
public:
typedef typename EOT::Fitness FitT;
/// Ctor: takes a length, and divides that length in equal parts
RoyalRoad( unsigned _div ): eoEvalFunc<EOT >(), div( _div ) {};
// Applies the function
virtual void operator() ( EOT & _eo ) {
FitT fitness = 0;
if (_eo.invalid()) {
for ( unsigned i = 0; i < _eo.size()/div; i ++ ) {
bool block = true;
for ( unsigned j = 0; j < div; j ++ ) {
block &= _eo[i*div+j];
}
if (block) {
fitness += div;
}
}
_eo.fitness( fitness );
}
};
private:
unsigned div;
};
#endif

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#include <algorithm>
//-----------------------------------------------------------------------------
/** Just the simple function that takes binary value of a chromosome and sets
the fitnes.
@param _chrom A binary chromosome
*/
template <class Chrom> double binary_value(const Chrom& _chrom)
{
double sum = 0.0;
for (unsigned i=0; i<_chrom.size(); i++)
sum += _chrom[i];
return sum;
}

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test/eo/boxplot.py Executable file
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#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 2:
print 'Usage: boxplot.py [Results files, ...]'
sys.exit()
for i in range(1, len(sys.argv)):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.show()

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test/eo/boxplot_to_pdf.py Executable file
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#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 3:
print 'Usage: boxplot_to_pdf.py [Results files, ...] [output file in .pdf]'
sys.exit()
for i in range(1, len(sys.argv) - 1):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.savefig( sys.argv[ len(sys.argv) - 1 ], format='pdf', transparent=True )

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test/eo/boxplot_to_png.py Executable file
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#!/usr/bin/env python
import pylab
import sys
if __name__ == '__main__':
if len(sys.argv) < 3:
print 'Usage: boxplot_to_png.py [Results files, ...] [output file in .png]'
sys.exit()
for i in range(1, len(sys.argv) - 1):
pylab.boxplot( [ [ float(value) for value in line.split() ] for line in open( sys.argv[i] ).readlines() ] )
pylab.xlabel('iterations')
pylab.savefig( sys.argv[ len(sys.argv) - 1 ], format='png', transparent=True, papertype='a0' )

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#include <map> // for pair
#include <iostream>
#include <stdexcept>
#include <vector>
#include <algorithm>
#include <math.h> // for exp
using namespace std;
/* fitness_traits.h */
// default traits: defaults to a double that needs to be maximized
template <class T = double>
struct fitness_traits
{
// Needs mapping can be used to figure out whether you need to do fitness scaling (or not)
const static bool needs_mapping = false;
// storage_type: what to store next to the genotype
typedef T storage_type;
// performance_type: what the eoEvalFunc calculates
typedef T performance_type;
// worth_type: what the scaling function does
typedef T worth_type;
// access_performance: how to get from what is stored to a mutable performance
static performance_type& access_performance(storage_type& a) { return a; }
// access_worth: how to get from what is stored to a mutable worth
static worth_type& access_worth(storage_type& a) { return a; }
// get_performance: from storage_type to a performance figure
static performance_type get_performance(storage_type a) { return a; }
// get_worth: from storage_type to a worth figure
static worth_type get_worth(storage_type a) { return a; }
// get the fitness out of the individual
template <class EOT>
static worth_type get_fitness(const EOT& _eo) { return _eo.performance(); }
// compare the two individuals
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.performance() > _eo2.performance();
}
};
struct minimization {};
struct maximization {};
struct fitness_traits<minimization> : public fitness_traits<double>
{
// for minimization, invert the is_better
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.performance() < _eo2.performance();
}
};
// for maximization, just take the default behaviour
struct fitness_traits<maximization> : public fitness_traits<double> {};
// forward declaration
//template <class EOT> class eoPop;
//template <class Fitness, class Traits> class EO;
// unfortunately, partial template specialization is not approved by Microsoft (though ANSI says it's ok)
// Probably need some macro-magic to make this work (MicroSoft == MacroHard)
// A pair class: first == performance, second == worth, redefine all types, data and functions
template <class Performance, class Worth>
struct fitness_traits< pair<Performance, Worth> >
{
typedef pair<Performance, Worth> storage_type;
typedef Performance performance_type;
typedef Worth worth_type;
const static bool needs_mapping = true;
static performance_type& access_performance(storage_type& a) { return a.first; }
static worth_type& access_worth(storage_type& a) { return a.second; }
static performance_type get_performance(const storage_type& a) { return a.first; }
static worth_type get_worth(const storage_type& a) { return a.second; }
// This function calls _eo.worth() which in turn checks the fitness flag and calls get_worth above
// The compiler should be able to inline all these calls and come up with a very compact solution
template <class EOT>
static worth_type get_fitness(const EOT& _eo) { return _eo.worth(); }
template <class EOT>
static bool is_better(const EOT& _eo1, const EOT& _eo2)
{
return _eo1.worth() > _eo2.worth();
}
};
/* end fitness_traits.h */
/* EO.h
The Fitness template argument is there for backward compatibility reasons
*/
template <class Fitness, class Traits = fitness_traits<Fitness> >
class EO
{
public :
typedef Traits fitness_traits;
typedef typename Traits::storage_type storage_type;
typedef typename Traits::performance_type performance_type;
typedef typename Traits::worth_type worth_type;
EO() : valid_performance(false), valid_worth(false), rep_fitness() {}
// for backwards compatibility
void fitness(performance_type perf)
{
performance(perf);
}
void performance(performance_type perf)
{
valid_performance = true;
Traits::access_performance(rep_fitness) = perf;
}
performance_type performance(void) const
{
if(!valid_performance) throw runtime_error("no performance");
return Traits::get_performance(rep_fitness);
}
void worth(worth_type worth)
{
valid_worth = true;
Traits::access_worth(rep_fitness) = worth;
}
worth_type worth(void) const
{
if(!valid_worth) throw runtime_error("no worth");
if(!Traits::needs_mapping) throw runtime_error("no mapping");
return Traits::get_worth(rep_fitness);
}
worth_type fitness(void) const
{
return Traits::get_fitness(*this);
}
void invalidate(void)
{
valid_performance = false;
valid_worth = false;
}
void invalidate_worth(void)
{
valid_worth = false;
}
bool operator<(const EO<Fitness, Traits>& other) const
{
return !Traits::is_better(other, *this);
}
bool operator>(const EO<Fitness, Traits>& other) const
{
return Traits::is_better(other, *this);
}
private :
bool valid_performance;
bool valid_worth;
storage_type rep_fitness;
};
/* end EO.h */
/* eoPerf2Worth.h */
// get the name known
template <class EOT> class eoPop;
template <class EOT>
void exponential_scaling(eoPop<EOT>& _pop)
{
for (unsigned i = 0; i < _pop.size(); ++i)
{ // change minimimization into maximization
_pop[i].worth(exp(-_pop[i].performance()));
}
}
template <class EOT>
class eoPerf2Worth /* : public eoUF<eoPop<EOT>&, void> */
{
public :
virtual void operator()(eoPop<EOT>& _pop)
{
return exponential_scaling(_pop);
}
};
/* end eoPerf2Worth.h */
/* eoPop.h */
template <class EOT>
class eoPop : public vector<EOT>
{
public :
typedef typename EOT::fitness_traits fitness_traits;
eoPop(void) : p2w(0) {}
void sort()
{
scale(); // get the worths up to date
std::sort(begin(), end(), greater<EOT>());
}
void scale()
{
if (p2w)
{
if (!fitness_traits::needs_mapping)
{
throw runtime_error("eoPop: no scaling needed, yet a scaling function is defined");
}
(*p2w)(*this);
}
else if (fitness_traits::needs_mapping)
{
throw runtime_error("eoPop: no scaling function attached to the population, while one was certainly called for");
}
}
void setPerf2Worth(eoPerf2Worth<EOT>& _p2w)
{
p2w = &_p2w;
}
void setPerf2Worth(eoPerf2Worth<EOT>* _p2w)
{
p2w = _p2w;
}
eoPerf2Worth<EOT>* getPerf2Worth() { return p2w; }
void swap(eoPop<EOT>& other)
{
vector<EOT>::swap(other);
eoPerf2Worth<EOT>* tmp = p2w;
p2w = other.p2w;
other.p2w = tmp;
}
private :
// a pointer as it can be emtpy
eoPerf2Worth<EOT>* p2w;
};
// need this one to be able to swap the members as well...
template <class EOT>
void swap(eoPop<EOT>& _p1, eoPop<EOT>& _p2)
{
_p1.swap(_p2);
}
/* end eoPop.h */
/* main and test */
template <class EOT>
void algo(eoPop<EOT>& _pop)
{
eoPop<EOT> offspring; // how to get the scaling info into this guy??
offspring.setPerf2Worth(_pop.getPerf2Worth()); // like this!
std::copy(_pop.begin(), _pop.end(), back_inserter(offspring));
offspring.sort(); // should call scale
swap(_pop, offspring);
}
void minimization_test()
{
typedef EO<minimization> eo_type;
eo_type eo1;
eo_type eo2;
eo1.performance(1.0);
eo2.performance(2.0);
std::cout << "With minimizing fitness" << std::endl;
std::cout << eo1.fitness() << " < " << eo2.fitness() << " returns " << (eo1 < eo2) << std::endl;
std::cout << eo2.fitness() << " < " << eo1.fitness() << " returns " << (eo2 < eo1) << std::endl;
}
void the_main()
{
typedef EO<double> simple_eo;
typedef EO<pair<double, double> > scaled_eo;
simple_eo eo1;
simple_eo eo3;
/* First test some simple comparisons */
eo1.fitness(10); // could also use performance()
eo3.fitness(5);
std::cout << eo1.fitness() << std::endl;
std::cout << eo3.fitness() << std::endl;
std::cout << "eo1 < eo3 = " << (eo1 < eo3) << std::endl;
scaled_eo eo2;
scaled_eo eo4;
eo2.performance(10);
eo4.performance(8);
/* Now test if the worth gets accessed and if the flag protects it */
try
{
std::cout << eo2.fitness() << std::endl;
std::cout << "did not throw" << std::endl;
assert(false); // should throw
}
catch(std::exception& e)
{
std::cout << "Fitness threw exception, as it should" << std::endl;
std::cout << e.what() << std::endl;
}
/* Set the worth and all is well (this is normally done by some perf2worth functor */
eo2.worth(3);
eo4.worth(5);
std::cout << "with maximization " << std::endl;
std::cout << eo2.fitness() << std::endl;
std::cout << eo4.fitness() << std::endl;
std::cout << eo2.fitness() << " < " << eo4.fitness() << " returns " << (eo2 < eo4) << std::endl;
/* Test the minimization of fitness */
minimization_test();
/* Populations */
// test pop without scaling, should have no overhead save for a single empty pointer in pop
eoPop<simple_eo> pop0;
pop0.resize(1);
pop0[0].fitness(1);
algo(pop0);
std::cout << pop0[0].fitness() << std::endl;
assert(pop0[0].fitness() == 1);
/* test pop with scaling */
eoPerf2Worth<scaled_eo> perf2worth;
eoPop<scaled_eo> pop1;
pop1.resize(1);
pop1[0].fitness(1.0); // emulate evaluation
// at this point getting the fitness should throw
try
{
std::cout << pop1[0].fitness() << std::endl;
std::cout << "did not throw" << std::endl;
assert(false); // should throw
}
catch(std::exception& e)
{
std::cout << "Fitness threw exception, as it should" << std::endl;
std::cout << e.what() << std::endl;
}
// at this point trying to scale should throw
try
{
algo(pop1); // should complain that it cannot scale
assert(false); // so it would never get here
}
catch(std::exception& e)
{ // but rather ends here
std::cout << e.what() << std::endl;
}
// ok, now set the scaling
pop1.setPerf2Worth(perf2worth);
algo(pop1);
std::cout << "the fitness has been transformed from " << pop1[0].performance() << " to exp(-1) = " << pop1[0].fitness() << std::endl;
}
int main()
{
try
{
the_main();
}
catch(std::exception& e)
{
std::cout << e.what() << std::endl;
}
}

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#include <vector>
//-----------------------------------------------------------------------------
/** Just a simple function that takes an eoEsBase<double> and sets the fitnes
to sphere
@param _ind vector<double>
*/
double real_value(const std::vector<double>& _ind)
{
double sum = 0;
for (unsigned i = 0; i < _ind.size(); i++)
sum += _ind[i] * _ind[i];
return sum/_ind.size();
}

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#!/bin/sh
echo "Testing -h"
./t-eoCheckpointing -h
echo "Finished"
#TODO test if an error occured
echo "Ok"

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test/eo/t-MGE-control.cpp Executable file
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//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo/ga/eoBitOp.h>
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
eoOneBitFlip<Chrom> vm;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.2);
propSel.add(xover, 0.8);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2 );
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

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test/eo/t-MGE.cpp Executable file
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//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
#include <paradiseo/eo/ga/eoBitOp.h>
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
VirusMutation<float> vm;
VirusTransmission<float> vt;
VirusBitFlip<float> vf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.1);
propSel.add(vf, 0.05);
propSel.add(vt, 0.05);
propSel.add(xover, 0.8);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (std::exception& e)
{
std::cout << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return 0;
}
//-----------------------------------------------------------------------------

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test/eo/t-MGE1bit.cpp Executable file
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//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <paradiseo/eo.h>
//#include "ga/eoBitOp.h"
#include "RoyalRoad.h"
// Viri
#include "VirusOp.h"
#include "eoVirus.h"
#include "eoInitVirus.h"
//-----------------------------------------------------------------------------
typedef eoVirus<double> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 10, CHROM_SIZE = 12;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
RoyalRoad<Chrom> rr( 8 );
eoEvalFuncCounter<Chrom> eval( rr );
eoInitVirus1bit<double> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
std::cout << "population:" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
// selection
eoStochTournamentSelect<Chrom> lottery(0.9 );
// breeder
VirusShiftMutation<double> vm;
VirusTransmission<double> vt;
VirusBitFlip<double> vf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.8);
propSel.add(vf, 0.05);
propSel.add(vt, 0.05);
propSel.add(xover, 0.1);
// Replace a single one
eoCommaReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add(continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
eoPopStat<Chrom> dumper( 10 );
monitor.add(stats);
checkpoint.add(dumper);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace);
// evolution
try {
ea(pop);
} catch (std::exception& e) {
std::cerr << "exception: " << e.what() << std::endl;;
exit(EXIT_FAILURE);
}
std::cout << "pop" << std::endl;
for (i = 0; i < pop.size(); ++i)
std::cout << "\t" << pop[i] << " " << pop[i].fitness() << std::endl;
std::cout << "\n --> Number of Evaluations = " << eval.getValue() << std::endl;
return EXIT_SUCCESS;
}
//-----------------------------------------------------------------------------
// Local Variables:
// mode: C++
// c-file-style: "Stroustrup"
// End:

14
test/eo/t-eo.cpp Executable file
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#include <paradiseo/eo.h>
typedef EO<float> Chrom;
int main()
{
Chrom chrom1, chrom2;
// EO objects can be printed with stream operators
std::cout << "chrom1 = " << chrom1 << std::endl
<< "chrom2 = " << chrom2 << std::endl;
return 0;
}

220
test/eo/t-eo2dVector.cc Executable file
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/*
-----------------------------------------------------------------------------
File............: t-eo2dVector.cc
Author..........: Geneura Team (this file: Victor Rivas, vrivas@ujaen.es)
Date............: 01-Oct-1999, at Fac. of Sciences, Univ. of Granada (Spain)
Description.....: Test for 2 dimensional eoVector.
================ Modif. 1 ================
Author........:
Date..........:
Description...:
-----------------------------------------------------------------------------
*/
#include <stdexcept>
#include <paradiseo/eo/eo2dVector.h> // eo2dVector
#include <paradiseo/eo/eoUniform.h> // Random generator
//-----------------------------------------------------------------------------
typedef unsigned T;
typedef double fitnessT;
typedef eo2dVector<T,fitnessT> C;
//-----------------------------------------------------------------------------
main()
{
{
C c1;
cout << "Default constructor: " << endl
<< c1 << endl;
}
{
C c1( 5,6,1 );
cout << "Default constructor with values: " << endl
<< c1 << endl;
}
{
eoUniform<T> aleat( 1,10 );
C c1( 5,6, aleat );
cout << "Random constructor: " << endl
<< c1 << endl;
}
{
C c1( 3,4,1 ), c2( c1 );
cout << "Copy constructor: " << endl
<< "Original chromosome: " << endl
<< c1 << endl
<< "Copy chromosome: " << endl
<< c2 << endl;
}
eoUniform<T> aleat( 1,10 );
C c1( 3,4,aleat );
cout << "-----------------------------------------------------" << endl
<< "Since now on all the operations are applied to " << endl
<< c1
<< "-----------------------------------------------------" << endl;
{
cout << "getGene(2,2): "
<< c1.getGene(2,2) << endl;
}
{
c1.setGene( 2,2,300 );
cout << "setGene(2,2,300): " << endl
<< c1 << endl;
}
{
unsigned u1=0, u3=333, u5=555;
vector<T> v1( 4,u1 ), v2( 4,u3 ), v3( 4,u5 );
c1.insertRow( 0,v1 );
c1.insertRow( 3,v2 );
c1.insertRow( 5,v3 );
cout << "Insert rows at positions 0, 3 and 5: " << endl
<< c1 << endl;
}
{
c1.deleteRow( 5 );
c1.deleteRow( 3 );
c1.deleteRow( 0 );
cout << "Delete rows at positions 5, 3 and 0: " << endl
<< c1 << endl;
}
{
unsigned u1=0, u3=333, u6=666;
vector<T> v1( 3,u1 ), v2( 3,u3 ), v3( 3,u6 );
c1.insertCol( 0,v1 );
c1.insertCol( 3,v2 );
c1.insertCol( 6,v3 );
cout << "Insert columns at positions 0, 3 and 6: " << endl
<< c1 << endl;
}
{
c1.deleteCol( 6 );
c1.deleteCol( 3 );
c1.deleteCol( 0 );
cout << "Delete columns at positions 6, 3 and 0: " << endl
<< c1 << endl;
}
{
cout << "Number of Rows: " << endl
<< c1.numOfRows() << endl;
}
{
cout << "Number of Columns: " << endl
<< c1.numOfCols() << endl;
}
{
cout << "Class Name: " << endl
<< c1.className() << endl;
}
cout << "-----------------------------------------------------" << endl
<< "Catching exceptions: " << endl
<< c1
<< "-----------------------------------------------------" << endl;
{
cout << "* Trying getGene(10,1): " << endl;
try {
c1.getGene( 10,1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying getGene(1,10): " << endl;
try {
c1.getGene( 1,10) ;
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying setGene( 10,1,999 ): " << endl;
try {
c1.setGene( 10,1,999 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying setGene( 1,10,999 ): " << endl;
try {
c1.setGene( 1,10,999 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 4, u1 );
cout << "* Trying insertRow( 10, v1 ): " << endl;
try {
c1.insertRow( 10,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 5, u1 );
cout << "* Trying insertRow( 1, v1 ) with v1.size()=5: " << endl;
try {
c1.insertRow( 1,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying deleteRow( 10 ): " << endl;
try {
c1.deleteRow( 10 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 3, u1 );
cout << "* Trying insertCol( 10,v1 ): " << endl;
try {
c1.insertCol( 10,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
unsigned u1=111;
vector<T> v1( 5, u1 );
cout << "* Trying insertCol( 1,v1 ) with v1.size()=5: " << endl;
try {
c1.insertCol( 1,v1 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
{
cout << "* Trying deleteCol( 10 ): " << endl;
try {
c1.deleteCol( 10 );
} catch (exception& e ) {
cerr << e.what() << endl;
}
}
}
//-----------------------------------------------------------------------------

127
test/eo/t-eoCMAES.cpp Executable file
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#include <iostream>
#include <paradiseo/eo.h>
/*
#include <paradiseo/eo/eoScalarFitness.h>
#include <paradiseo/eo/eoVector.h>
#include <paradiseo/eo/eoPop.h>
#include <paradiseo/eo/utils/eoParser.h>
#include <paradiseo/eo/utils/eoCheckPoint.h>
#include <paradiseo/eo/eoEvalFuncPtr.h>
#include <paradiseo/eo/eoGenContinue.h>
#include <paradiseo/eo/eoFitContinue.h>
#include <paradiseo/eo/utils/eoStdoutMonitor.h>
#include <paradiseo/eo/utils/eoStat.h>
#include <paradiseo/eo/utils/eoTimedMonitor.h>
#include <paradiseo/eo/eoMergeReduce.h>
#include <paradiseo/eo/eoEasyEA.h>
#include <paradiseo/eo/es/CMAState.h>
#include <paradiseo/eo/es/CMAParams.h>
#include <paradiseo/eo/es/eoCMAInit.h>
#include <paradiseo/eo/es/eoCMABreed.h>
*/
using namespace eo;
using namespace std;
typedef eoMinimizingFitness FitT;
typedef eoVector<FitT, double> EoType;
double sqr(double x) { return x*x; }
eoValueParam<int> evals(0,"Function Evals","Number of Evaluations");
double f_sphere(const vector<double>& values) {
double sum = 0.0;
for (unsigned i = 0; i < values.size(); ++i) {
sum += values[i] * values[i];
}
++evals.value();
return sum;
}
double f_rosen(const vector<double>& x) {
double sum =0.0;
for (unsigned i = 0; i < x.size()-1; ++i) {
sum += 100 * sqr(sqr(x[i])-x[i+1]) + sqr(1.-x[i]);
}
++evals.value();
return sum;
}
int main(int argc, char* argv[]) {
// make sure we have a dimensionality parameter (for testing)
char** rargv = new char*[argc+1];
rargv[0] = argv[0];
rargv[1] = (char*)"-N10";
for (int i = 2; i < argc; ++i) {
rargv[i] = argv[i-1];
}
eoParser parser(argc+1, rargv);
CMAParams params(parser);
vector<double> initial_point(params.n, 0.0);
CMAState state(params, initial_point);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
return 1;
}
eoCMAInit<FitT> init(state);
eoPop<EoType> pop(params.mu, init);
eoEvalFuncPtr<EoType, double, const vector<double>&> eval( f_rosen );
eoCMABreed<FitT> breed(state, params.lambda);
for (unsigned i = 0; i < pop.size(); ++i) {
eval(pop[i]);
}
eoCommaReplacement<EoType> comma;
eoGenContinue<EoType> gen(params.maxgen);
eoFitContinue<EoType> fit(1e-10);
eoCheckPoint<EoType> checkpoint(gen);
checkpoint.add(fit);
eoBestFitnessStat<EoType> stat;
eoStdoutMonitor mon;
mon.add(stat);
mon.add(evals);
eoTimedMonitor timed(1);// 1 seconds
timed.add(mon); // wrap it
checkpoint.add(timed);
checkpoint.add(stat);
eoEasyEA<EoType> algo(
checkpoint,
eval,
breed,
comma);
algo(pop);
pop.sort();
cout << pop[0] << endl;
cout << "Fitness achieved = " << pop[0].fitness() << endl;
cout << "Function evaluations = " << evals.value() << endl;
}

177
test/eo/t-eoCheckpointing.cpp Executable file
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// to avoid long name warnings
#ifdef _MSC_VER
#pragma warning(disable:4786)
#endif
#include <stdexcept> // runtime_error
#include <paradiseo/eo.h>
// general
/*
#include <paradiseo/eo/utils/eoRNG.h> // Random number generators
#include <paradiseo/eo/ga.h>
#include <paradiseo/eo/utils/eoParser.h>
#include <paradiseo/eo/utils/eoState.h>
#include <paradiseo/eo/eoGenContinue.h>
// include package checkpointing
#include <paradiseo/eo/utils/checkpointing>
*/
struct Dummy : public EO<double>
{
typedef double Type;
};
struct eoDummyPop : public eoPop<Dummy>
{
public :
eoDummyPop(int s = 2) { resize(s); }
};
int the_main(int argc, char **argv)
{ // ok, we have a command line parser and a state
typedef eoBit<float> Chrom;
eoParser parser(argc, argv);
// Define Parameters
eoValueParam<double> rate(0.01, "mutationRatePerBit", "Initial value for mutation rate per bit");
eoValueParam<double> factor(0.99, "mutationFactor", "Decrease factor for mutation rate");
eoValueParam<uint32_t> seed(time(0), "seed", "Random number seed");
eoValueParam<std::string> load_name("", "Load","Load",'L');
eoValueParam<std::string> save_name("", "Save","Save",'S');
// Register them
parser.processParam(rate, "Genetic Operators");
parser.processParam(factor, "Genetic Operators");
parser.processParam(load_name, "Persistence");
parser.processParam(save_name, "Persistence");
parser.processParam(seed, "Rng seeding");
eoState state;
state.registerObject(parser);
if (load_name.value() != "")
{ // load the parser. This is only neccessary when the user wants to
// be able to change the parameters in the state file by hand.
state.load(load_name.value()); // load the parser
}
// Create the algorithm here
typedef Dummy EoType;
eoDummyPop pop;
eoGenContinue<EoType> genTerm(5); // run for 5 generations
eoCheckPoint<EoType> checkpoint(genTerm);
// The algorithm will now quit after five generations
// Create a counter parameter
eoValueParam<unsigned> generationCounter(0, "Generation");
// Create an incrementor (wich is an eoUpdater). Note that the
// Parameter's value is passed by reference, so every time the incrementer increments,
// the data in generationCounter will change.
eoIncrementor<unsigned> increment(generationCounter.value());
// Add it to the checkpoint, this will result in the counter being incremented every generation
checkpoint.add(increment);
// The file monitor will print parameters to a comma seperated file
eoFileMonitor monitor("monitor.csv");
// the checkpoint mechanism can handle multiple monitors
checkpoint.add(monitor);
// the monitor can monitor parameters such as the generationCounter
monitor.add(generationCounter);
// Second moment stats: average and stdev
eoSecondMomentStats<EoType> stats;
// Add it to the checkpoint to get it called at the appropriate time
checkpoint.add(stats);
// Add it to the monitor to get it written to the file
monitor.add(stats);
// save state every third generation
eoCountedStateSaver stateSaver1(3, state, "generation");
// save state every 2 seconds
eoTimedStateSaver stateSaver2(2, state, "time");
// And add the two savers to the checkpoint
checkpoint.add(stateSaver1);
checkpoint.add(stateSaver2);
// Register the algorithm
state.registerObject(rng);
state.registerObject(pop);
if (parser.userNeedsHelp())
{
parser.printHelp(std::cout);
return 0;
}
// Either load or initialize
if (load_name.value() != "")
{
state.load(load_name.value()); // load the rest
}
else
{
// else
// initialize rng and population
rng.reseed(seed.value());
pop.resize(2);
pop[0].fitness(1);
pop[1].fitness(2);
}
while(checkpoint(pop))
{
pop[0].fitness(pop[0].fitness() + 1);
time_t now = time(0);
while (time(0) == now) {} // wait a second to test timed saver
std::cout << "gen " << generationCounter.value() << std::endl;
}
// run the algorithm
// Save when needed
if (save_name.value() != "")
{
std::string file_name = save_name.value();
save_name.value() = ""; // so that it does not appear in the parser section of the state file
state.save(file_name);
}
return 1;
}
int main(int argc, char **argv)
{
try
{
the_main(argc, argv);
}
catch(std::exception& e)
{
std::cout << "Exception: " << e.what() << std::endl;
}
}

88
test/eo/t-eoDualFitness.cpp Executable file
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#include <utility>
#include <paradiseo/eo.h>
#include <paradiseo/eo/es.h>
#include <paradiseo/eo/utils/eoStat.h>
typedef eoVector<eoDualFitness<double,eoMinimizingFitness>,double> DualVector;
template<class EOT>
class DualSphere : public eoEvalFunc<EOT>
{
public:
virtual void operator()( EOT & x )
{
if( x.invalid() ) { return; }
double sum = 0;
int sign = 1;
for( unsigned int i=0, s=x.size(); i<s; ++i ) {
sum += x[i] * x[i];
sign *= x[i]<0 ? -1 : 1;
}
x.fitness( std::make_pair( sum, sign>0 ? true : false ) );
}
};
double test( eoPop<DualVector>& pop, double target_value )
{
DualSphere<DualVector> eval;
eoPopLoopEval<DualVector> pop_eval(eval);
pop_eval(pop,pop);
eoInterquartileRangeStat<DualVector> iqr_stat( std::make_pair(0.0,false), "IQR" );
iqr_stat( pop );
std::cout << iqr_stat.longName() << "=" << iqr_stat.value() << " should be " << target_value << std::endl;
return iqr_stat.value().value();
}
int main()
{
eoPop<DualVector> pop;
// fixed test
DualVector sol1(2,-1);
DualVector sol2(2,-1);
DualVector sol3(2,1);
DualVector sol4(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
// on the sphere function everyone has the same fitness of 1
if( test(pop, 0) != 0 ) {
exit(1);
}
pop.erase(pop.begin(),pop.end());
// fixed test
sol1 = DualVector(2,0);
sol2 = DualVector(2,0);
sol3 = DualVector(2,1);
sol4 = DualVector(2,1);
pop.push_back( sol1 );
pop.push_back( sol2 );
pop.push_back( sol3 );
pop.push_back( sol4 );
if( test(pop, 1) != 1 ) {
exit(1);
}
// test on a random normal distribution
eoNormalGenerator<double> normal(1,rng);
eoInitFixedLength<DualVector> init_N(2, normal);
pop = eoPop<DualVector>( 1000000, init_N );
double iqr = test(pop, 1.09);
if( iqr < 1.08 || iqr > 1.11 ) {
exit(1);
}
}

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