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Merge branch 'master' of /tools/eo

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This commit is contained in:
Benjamin Bouvier 2012-07-27 15:10:07 +02:00
commit 11f01d5a53
108 changed files with 8642 additions and 1297 deletions
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1
eo/CMakeLists.txt
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@ -1,3 +1,4 @@
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
######################################################################################
### 0) If you want to set your variables in eo-conf.cmake and avoid the cmd line

45
eo/ForRelease
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@ -1,45 +0,0 @@
In order to create a new release from the current repository, perform the
following steps:
- If necessary, create a branch named "eo_x.y.z"
- Set version number in eo-conf.cmake
- Check/update NEWS file, set release date and version in NEWS.
- use the "archive_current.sh" script to create the source archive
- Build the packages
- Put source archive and packages files at SourceForge
- Post news on SourceForge project-page
- Send announcement to mailing lists
- Bump version number to next "x.y.z-edge" in eo-conf.cmake
When reaching stable versions:
- prepare a message with the following template:
-----8<-----
A new version of the "Evolving Objects" framework is available.
EO is a template-based, C++ evolutionary computation library which
helps you to write your own stochastic optimization algorithms
insanely fast.
Learn more about EO on the official website:
http://eodev.sourceforge.net/
You will find the release x.y.z at the following address:
https://sourceforge.net/projects/eodev/files/eo/
Here is a summary of the change log:
- XXXXX
- and more…
Do not hesitate to submit the bugs you will face:
https://sourceforge.net/apps/trac/eodev/wiki/WikiStart
Happy evolutionary hacking.
-----8<-----
- Post the message to:
- EO news https://sourceforge.net/news/?group_id=9775
- EO mailing list: eodev-main@lists.sourceforge.net
- ParadisEO mailing list: paradiseo-users@lists.gforge.inria.fr
- EC-digest maling list: ec-digest-l@listserv.gmu.edu
- JET mailing list: jet@inria.fr

37
eo/NEWS
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@ -1,4 +1,29 @@
* current version
* current release:
* release 1.3.1 (2012-07-27)
- the eo::mpi modules is no longer dependent from boost::mpi
- parallel multi-start example
- bugfix: an error is now thrown when accessing best_element of an empty population
* release 1.3.0 (2012-07-24)
- features:
- delete the deprecated code parts (was marked as deprecated in the release 1.1)
- eoSignal: a class to handle signal with eoCheckpoint instances
- eoDetSingleBitFlip: bit flip mutation that changes exactly k bits while checking for duplicate
- eoFunctorStat: a wrapper to turn any stand-alone function and into an eoStat
- generilazed the output of an eoState: now you can change the format, comes with defaults formatting (latex and json)
- eoWrongParamTypeException: a new exception to handle cases where a wrong template is given to eoParser::valueOf
- added a getParam method to the eoParser, that raise an exception if the parameter has not been declared
- eoParserLogger features are now included in the default eoParser
- build system:
- improvements of the build architecture
- create PKGBUILD file for archlinux package manager
- a FindEO module for CMake
- bugfixes:
- fixed regression with gcc 4.7
- fixed compilation issues in Microsoft Visual C++, related to time measurement
- added several asserts accross the framework (note: asserts are included only in debug mode)
- lot of small bugfixes :-)
* release 1.2 (16. May. 2011)
- fixed the incremental allocation issue in variation operators which were
@ -20,11 +45,11 @@
- GCC 4.3 compatibility
- new versatile log system with several nested verbose levels
- classes using intern verbose parameters marked as deprecated, please update your code accordingly if you use one of the following files:
eo/src/eoCombinedInit.h
eo/src/eoGenContinue.h
eo/src/eoProportionalCombinedOp.h
eo/src/utils/eoData.h
eo/src/utils/eoStdoutMonitor.h
eo/src/eoCombinedInit.h
eo/src/eoGenContinue.h
eo/src/eoProportionalCombinedOp.h
eo/src/utils/eoData.h
eo/src/utils/eoStdoutMonitor.h
- an evaluator that throw an exception if a maximum eval numbers has been reached, independently of the number of generations
- new monitor that can write on any ostream
- new continuator that can catch POSIX system user signals

2
eo/doc/index.h
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@ -5,7 +5,7 @@
The best place to learn about the features and approaches of %EO with the help of examples is to look at
the <a href="../../tutorial/html/eoTutorial.html">tutorial</a>.
Once you have understand the @ref design of %EO, you could search for advanced features by browsing the <a
Once you have understand the @ref design of %EO, you can search for advanced features by browsing the <a
href="modules.html">modules</a> page.

3
eo/eo-conf.cmake
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@ -2,9 +2,10 @@
# Current version
SET(PROJECT_VERSION_MAJOR 1)
SET(PROJECT_VERSION_MINOR 3)
SET(PROJECT_VERSION_PATCH 0)
SET(PROJECT_VERSION_PATCH 2)
SET(PROJECT_VERSION_MISC "-edge")
# ADD_DEFINITIONS(-DDEPRECATED_MESSAGES) # disable warning deprecated function messages
# If you plan to use OpenMP, put the following boolean to true :
SET(WITH_OMP FALSE CACHE BOOL "Use OpenMP ?" FORCE)

30
eo/install_symlink.py.cmake
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@ -9,8 +9,8 @@ PREFIX = "/usr"
DATA = {
'dirs': [ "%s/share/%s" % (PREFIX, NAME) ],
'links': [ ("%s/src" % SOURCE, "%s/include/%s" % (PREFIX, NAME)),
("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
]
}
@ -21,19 +21,27 @@ import os, sys
def isroot():
if os.getuid() != 0:
print '[WARNING] you have to be root'
return False
print('[WARNING] you have to be root')
return False
return True
def uninstall():
for dummy, link in DATA['links']: os.remove(link)
for dirname in DATA['dirs']: os.rmdir(dirname)
print 'All symlinks have been removed.'
print('All symlinks have been removed.')
def install():
for dirname in DATA['dirs']: os.mkdir(dirname)
for src, dst in DATA['links']: os.symlink(src, dst)
print 'All symlinks have been installed.'
for dirname in DATA['dirs']:
try:
os.makedirs(dirname)
except(os.error):
pass
for src, dst in DATA['links']:
try:
os.symlink(src, dst)
except:
pass
print('All symlinks have been installed.')
def data():
from pprint import pprint
@ -41,11 +49,11 @@ def data():
if __name__ == '__main__':
if not isroot():
sys.exit()
sys.exit()
if len(sys.argv) < 2:
print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
sys.exit()
print(('Usage: %s [install|uninstall|data]' % sys.argv[0]))
sys.exit()
if sys.argv[1] == 'install': install()
elif sys.argv[1] == 'uninstall': uninstall()

3
eo/src/CMakeLists.txt
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@ -11,7 +11,8 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
IF(WITH_MPI)
MESSAGE("[EO] Compilation with MPI.")
SET(CMAKE_CXX_COMPILER "${MPI_DIR}/bin/mpicxx")
#SET(CMAKE_CXX_COMPILER "${MPI_DIR}/bin/mpicxx")
SET(CMAKE_CXX_COMPILER mpicxx)
# headers location
INCLUDE_DIRECTORIES(${MPI_DIR}/include)

21
eo/src/apply.h
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@ -19,7 +19,7 @@
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
mak@dhi.dk
mak@dhi.dk
*/
//-----------------------------------------------------------------------------
@ -31,7 +31,10 @@
#include <utils/eoLogger.h>
#include <eoFunctor.h>
#include <vector>
#ifdef _OPENMP
#include <omp.h>
#endif
/**
Applies a unary function to a std::vector of things.
@ -55,14 +58,26 @@ void apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
if (!eo::parallel.isDynamic())
{
#pragma omp parallel for if(eo::parallel.isEnabled()) //default(none) shared(_proc, _pop, size)
#ifdef _MSC_VER
//Visual Studio supports only OpenMP version 2.0 in which
//an index variable must be of a signed integral type
for (long long i = 0; i < size; ++i) { _proc(_pop[i]); }
#else // _MSC_VER
for (size_t i = 0; i < size; ++i) { _proc(_pop[i]); }
#endif
}
else
{
#pragma omp parallel for schedule(dynamic) if(eo::parallel.isEnabled())
#ifdef _MSC_VER
//Visual Studio supports only OpenMP version 2.0 in which
//an index variable must be of a signed integral type
for (long long i = 0; i < size; ++i) { _proc(_pop[i]); }
#else // _MSC_VER
//doesnot work with gcc 4.1.2
//default(none) shared(_proc, _pop, size)
for (size_t i = 0; i < size; ++i) { _proc(_pop[i]); }
#endif
}
if ( eo::parallel.enableResults() )
@ -94,7 +109,7 @@ void apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
// //default(none) shared(_proc, _pop, size)
// for (size_t i = 0; i < size; ++i)
// {
// _proc(_pop[i]);
// _proc(_pop[i]);
// }
// }
@ -112,7 +127,7 @@ void apply(eoUF<EOT&, void>& _proc, std::vector<EOT>& _pop)
// //default(none) shared(_proc, _pop, size)
// for (size_t i = 0; i < size; ++i)
// {
// _proc(_pop[i]);
// _proc(_pop[i]);
// }
// }

607
eo/src/do/make_checkpoint.h
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@ -1,45 +1,32 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// make_checkpoint.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 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 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.
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
mkeijzer@dhi.dk
*/
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
mkeijzer@dhi.dk
*/
//-----------------------------------------------------------------------------
#ifndef _make_checkpoint_h
#define _make_checkpoint_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@ -52,521 +39,315 @@
#include <eoEvalFuncCounter.h>
#include <utils/checkpointing>
// at the moment, in utils/make_help.cpp
// this should become some eoUtils.cpp with corresponding eoUtils.h
bool testDirRes(std::string _dirName, bool _erase);
/////////////////// The checkpoint and other I/O //////////////
/**
*
* CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested
* in the value of the parameter calculated on the evaluation function, not in the actual function itself!!
*
* @ingroup Builders
*/
*/
template <class EOT>
eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue)
{
// first, create a checkpoint from the eoContinue
eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue);
// first, create a checkpoint from the eoContinue
eoCheckPoint<EOT> *checkpoint = new eoCheckPoint<EOT>(_continue);
_state.storeFunctor(checkpoint);
_state.storeFunctor(checkpoint);
////////////////////
// Signal monitoring
////////////////////
#ifndef _MSC_VER
// the CtrlC monitoring interception
eoSignal<EOT> *mon_ctrlCCont;
eoValueParam<bool>& mon_ctrlCParam = _parser.createParam(false, "monitor-with-CtrlC", "Monitor current generation upon Ctrl C",0, "Stopping criterion");
if (mon_ctrlCParam.value())
{
mon_ctrlCCont = new eoSignal<EOT>;
// store
_state.storeFunctor(mon_ctrlCCont);
// add to checkpoint
checkpoint->add(*mon_ctrlCCont);
}
#endif
///////////////////
// Counters
//////////////////
///////////////////
// is nb Eval to be used as counter?
eoValueParam<bool>& useEvalParam = _parser.createParam(true, "useEval", "Use nb of eval. as counter (vs nb of gen.)", '\0', "Output");
eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
// if we want the time, we need an eoTimeCounter
eoTimeCounter * tCounter = NULL;
// Counters
//////////////////
// is nb Eval to be used as counter?
eoValueParam<bool>& useEvalParam = _parser.createParam(true, "useEval", "Use nb of eval. as counter (vs nb of gen.)", '\0', "Output");
eoValueParam<bool>& useTimeParam = _parser.createParam(true, "useTime", "Display time (s) every generation", '\0', "Output");
// if we want the time, we need an eoTimeCounter
eoTimeCounter * tCounter = NULL;
// Create anyway a generation-counter
// Recent change (03/2002): it is now an eoIncrementorParam, both
// a parameter AND updater so you can store it into the eoState
eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
// store it in the state
_state.storeFunctor(generationCounter);
// And add it to the checkpoint,
checkpoint->add(*generationCounter);
// Create anyway a generation-counter
// Recent change (03/2002): it is now an eoIncrementorParam, both
// a parameter AND updater so you can store it into the eoState
eoIncrementorParam<unsigned> *generationCounter = new eoIncrementorParam<unsigned>("Gen.");
// store it in the state
_state.storeFunctor(generationCounter);
// And add it to the checkpoint,
checkpoint->add(*generationCounter);
// dir for DISK output
eoValueParam<std::string>& dirNameParam = _parser.createParam(std::string("Res"), "resDir", "Directory to store DISK outputs", '\0', "Output - Disk");
// shoudl we empty it if exists
eoValueParam<bool>& eraseParam = _parser.createParam(true, "eraseDir", "erase files in dirName if any", '\0', "Output - Disk");
bool dirOK = false; // not tested yet
/////////////////////////////////////////
// now some statistics on the population:
/////////////////////////////////////////
/**
* existing stats as of today, April 10. 2001
*
* eoBestFitnessStat : best value in pop - type EOT::Fitness
* eoAverageStat : average value in pop - type EOT::Fitness
* eoSecondMomentStat: average + stdev - type std::pair<double, double>
* eoSortedPopStat : whole population - type std::string (!!)
* eoScalarFitnessStat: the fitnesses - type std::vector<double>
*/
// Best fitness in population
//---------------------------
eoValueParam<bool>& printBestParam = _parser.createParam(true, "printBestStat", "Print Best/avg/stdev every gen.", '\0', "Output");
eoValueParam<bool>& plotBestParam = _parser.createParam(false, "plotBestStat", "Plot Best/avg Stat", '\0', "Output - Graphical");
eoValueParam<bool>& fileBestParam = _parser.createParam(false, "fileBestStat", "Output bes/avg/std to file", '\0', "Output - Disk");
eoBestFitnessStat<EOT> *bestStat = NULL;
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() )
// we need the bestStat for at least one of the 3 above
{
bestStat = new eoBestFitnessStat<EOT>;
// store it
_state.storeFunctor(bestStat);
// add it to the checkpoint
checkpoint->add(*bestStat);
}
// we need the bestStat for at least one of the 3 above
{
bestStat = new eoBestFitnessStat<EOT>;
// store it
_state.storeFunctor(bestStat);
// add it to the checkpoint
checkpoint->add(*bestStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*bestStat);
}
// Average fitness alone
//----------------------
eoAverageStat<EOT> *averageStat = NULL; // do we need averageStat?
if ( plotBestParam.value() ) // we need it for gnuplot output
{
averageStat = new eoAverageStat<EOT>;
// store it
_state.storeFunctor(averageStat);
// add it to the checkpoint
checkpoint->add(*averageStat);
}
if ( printBestParam.value() || plotBestParam.value() || fileBestParam.value() ) // we need it for gnuplot output
{
averageStat = new eoAverageStat<EOT>;
// store it
_state.storeFunctor(averageStat);
// add it to the checkpoint
checkpoint->add(*averageStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*averageStat);
}
// Second moment stats: average and stdev
//---------------------------------------
eoSecondMomentStats<EOT> *secondStat = NULL;
if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
{
secondStat = new eoSecondMomentStats<EOT>;
// store it
_state.storeFunctor(secondStat);
// add it to the checkpoint
checkpoint->add(*secondStat);
}
if ( printBestParam.value() || fileBestParam.value() ) // we need it for screen output or file output
{
secondStat = new eoSecondMomentStats<EOT>;
// store it
_state.storeFunctor(secondStat);
// add it to the checkpoint
checkpoint->add(*secondStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*secondStat);
}
// Dump of the whole population
//-----------------------------
eoSortedPopStat<EOT> *popStat = NULL;
eoValueParam<bool>& printPopParam = _parser.createParam(false, "printPop", "Print sorted pop. every gen.", '\0', "Output");
if ( printPopParam.value() ) // we do want pop dump
{
popStat = new eoSortedPopStat<EOT>;
// store it
_state.storeFunctor(popStat);
// add it to the checkpoint
checkpoint->add(*popStat);
}
{
popStat = new eoSortedPopStat<EOT>;
// store it
_state.storeFunctor(popStat);
// add it to the checkpoint
checkpoint->add(*popStat);
// check if monitoring with signal
if ( mon_ctrlCParam.value() )
mon_ctrlCCont->add(*popStat);
}
// do we wnat some histogram of fitnesses snpashots?
eoValueParam<bool> plotHistogramParam = _parser.createParam(false, "plotHisto", "Plot histogram of fitnesses", '\0', "Output - Graphical");
///////////////
// The monitors
///////////////
// do we want an eoStdoutMonitor?
bool needStdoutMonitor = printBestParam.value()
|| printPopParam.value() ;
// The Stdout monitor will print parameters to the screen ...
if ( needStdoutMonitor )
{
eoStdoutMonitor *monitor = new eoStdoutMonitor(/*false FIXME remove this deprecated prototype*/);
_state.storeFunctor(monitor);
{
// when called by the checkpoint (i.e. at every generation)
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*monitor);
else
mon_ctrlCCont->add(*monitor);
eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
// the monitor will output a series of parameters: add them
monitor->add(*generationCounter);
_state.storeFunctor(monitor);
// when called by the checkpoint (i.e. at every generation)
checkpoint->add(*monitor);
// the monitor will output a series of parameters: add them
monitor->add(*generationCounter);
if (useEvalParam.value()) // we want nb of evaluations
monitor->add(_eval);
if (useTimeParam.value()) // we want time
{
tCounter = new eoTimeCounter;
_state.storeFunctor(tCounter);
checkpoint->add(*tCounter);
monitor->add(*tCounter);
}
if (printBestParam.value())
{
monitor->add(*bestStat);
monitor->add(*secondStat);
}
if ( printPopParam.value())
monitor->add(*popStat);
}
if (useEvalParam.value()) // we want nb of evaluations
monitor->add(_eval);
if (useTimeParam.value()) // we want time
{
tCounter = new eoTimeCounter;
_state.storeFunctor(tCounter);
// check if monitoring with signal
if ( ! mon_ctrlCParam.value() )
checkpoint->add(*tCounter);
else
mon_ctrlCCont->add(*tCounter);
monitor->add(*tCounter);
}
if (printBestParam.value())
{
monitor->add(*bestStat);
monitor->add(*secondStat);
}
if ( printPopParam.value())
monitor->add(*popStat);
}
// first handle the dir test - if we need at least one file
if ( ( fileBestParam.value() || plotBestParam.value() ||
plotHistogramParam.value() )
&& !dirOK ) // just in case we add something before
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
if (fileBestParam.value()) // A file monitor for best & secondMoment
{
{
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\best.xg";
std::string stmp = dirNameParam.value() + "\best.xg";
#else
std::string stmp = dirNameParam.value() + "/best.xg";
std::string stmp = dirNameParam.value() + "/best.xg";
#endif
eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
// save and give to checkpoint
_state.storeFunctor(fileMonitor);
checkpoint->add(*fileMonitor);
// and feed with some statistics
fileMonitor->add(*generationCounter);
fileMonitor->add(_eval);
if (tCounter) // we want the time as well
{
// std::cout << "On met timecounter\n";
fileMonitor->add(*tCounter);
}
fileMonitor->add(*bestStat);
fileMonitor->add(*secondStat);
}
eoFileMonitor *fileMonitor = new eoFileMonitor(stmp);
// save and give to checkpoint
_state.storeFunctor(fileMonitor);
checkpoint->add(*fileMonitor);
// and feed with some statistics
fileMonitor->add(*generationCounter);
fileMonitor->add(_eval);
if (tCounter) // we want the time as well
{
// std::cout << "On met timecounter\n";
fileMonitor->add(*tCounter);
}
fileMonitor->add(*bestStat);
fileMonitor->add(*secondStat);
}
#if defined(HAVE_GNUPLOT)
if (plotBestParam.value()) // an eoGnuplot1DMonitor for best & average
{
std::string stmp = dirNameParam.value() + "/gnu_best.xg";
eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
// save and give to checkpoint
_state.storeFunctor(gnuMonitor);
checkpoint->add(*gnuMonitor);
// and feed with some statistics
if (useEvalParam.value()) // do we want eval as X coordinate
gnuMonitor->add(_eval);
else if (tCounter) // or time?
gnuMonitor->add(*tCounter);
else // default: generation
gnuMonitor->add(*generationCounter);
gnuMonitor->add(*bestStat);
gnuMonitor->add(*averageStat);
}
{
std::string stmp = dirNameParam.value() + "/gnu_best.xg";
eoGnuplot1DMonitor *gnuMonitor = new eoGnuplot1DMonitor(stmp,minimizing_fitness<EOT>());
// save and give to checkpoint
_state.storeFunctor(gnuMonitor);
checkpoint->add(*gnuMonitor);
// and feed with some statistics
if (useEvalParam.value()) // do we want eval as X coordinate
gnuMonitor->add(_eval);
else if (tCounter) // or time?
gnuMonitor->add(*tCounter);
else // default: generation
gnuMonitor->add(*generationCounter);
gnuMonitor->add(*bestStat);
gnuMonitor->add(*averageStat);
}
// historgram?
if (plotHistogramParam.value()) // want to see how the fitness is spread?
{
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
_state.storeFunctor(fitStat);
checkpoint->add(*fitStat);
// a gnuplot-based monitor for snapshots: needs a dir name
eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
_state.storeFunctor(fitSnapshot);
// add any stat that is a std::vector<double> to it
fitSnapshot->add(*fitStat);
// and of course add it to the checkpoint
checkpoint->add(*fitSnapshot);
}
{
eoScalarFitnessStat<EOT> *fitStat = new eoScalarFitnessStat<EOT>;
_state.storeFunctor(fitStat);
checkpoint->add(*fitStat);
// a gnuplot-based monitor for snapshots: needs a dir name
eoGnuplot1DSnapshot *fitSnapshot = new eoGnuplot1DSnapshot(dirNameParam.value());
_state.storeFunctor(fitSnapshot);
// add any stat that is a std::vector<double> to it
fitSnapshot->add(*fitStat);
// and of course add it to the checkpoint
checkpoint->add(*fitSnapshot);
}
#endif
//////////////////////////////////
// State savers
//////////////////////////////
// feed the state to state savers
// save state every N generation
eoValueParam<unsigned>& saveFrequencyParam = _parser.createParam(unsigned(0), "saveFrequency", "Save every F generation (0 = only final state, absent = never)", '\0', "Persistence" );
if (_parser.isItThere(saveFrequencyParam))
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
unsigned freq = (saveFrequencyParam.value()>0 ? saveFrequencyParam.value() : UINT_MAX );
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\generations";
std::string stmp = dirNameParam.value() + "\generations";
#else
std::string stmp = dirNameParam.value() + "/generations";
std::string stmp = dirNameParam.value() + "/generations";
#endif
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
_state.storeFunctor(stateSaver1);
checkpoint->add(*stateSaver1);
}
eoCountedStateSaver *stateSaver1 = new eoCountedStateSaver(freq, _state, stmp);
_state.storeFunctor(stateSaver1);
checkpoint->add(*stateSaver1);
}
// save state every T seconds
eoValueParam<unsigned>& saveTimeIntervalParam = _parser.createParam(unsigned(0), "saveTimeInterval", "Save every T seconds (0 or absent = never)", '\0',"Persistence" );
if (_parser.isItThere(saveTimeIntervalParam) && saveTimeIntervalParam.value()>0)
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
{
// first make sure dirName is OK
if (! dirOK )
dirOK = testDirRes(dirNameParam.value(), eraseParam.value()); // TRUE
#ifdef _MSVC
std::string stmp = dirNameParam.value() + "\time";
std::string stmp = dirNameParam.value() + "\time";
#else
std::string stmp = dirNameParam.value() + "/time";
std::string stmp = dirNameParam.value() + "/time";
#endif
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2);
checkpoint->add(*stateSaver2);
}
eoTimedStateSaver *stateSaver2 = new eoTimedStateSaver(saveTimeIntervalParam.value(), _state, stmp);
_state.storeFunctor(stateSaver2);
checkpoint->add(*stateSaver2);
}
// and that's it for the (control and) output
return *checkpoint;
}
#endif

2
eo/src/do/make_checkpoint_FDC.h
View file

@ -175,7 +175,7 @@ eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEval
// The Stdout monitor will print parameters to the screen ...
if ( needStdoutMonitor )
{
eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
eoStdoutMonitor *monitor = new eoStdoutMonitor(/*false FIXME remove this deprecated prototype*/);
_state.storeFunctor(monitor);
// when called by the checkpoint (i.e. at every generation)

2
eo/src/do/make_checkpoint_assembled.h
View file

@ -129,7 +129,7 @@ eoCheckPoint<EOT>& do_make_checkpoint_assembled(eoParser& _parser, eoState& _sta
// STDOUT
// ------
eoStdoutMonitor *monitor = new eoStdoutMonitor(false);
eoStdoutMonitor *monitor = new eoStdoutMonitor(/*false FIXME remove this deprecated prototype*/);
_state.storeFunctor(monitor);
checkpoint->add(*monitor);
monitor->add(*generationCounter);

1
eo/src/eo
View file

@ -102,6 +102,7 @@
#include <eoSharingSelect.h>
// Embedding truncation selection
#include <eoTruncatedSelectOne.h>
#include <eoRankMuSelect.h>
// the batch selection - from an eoSelectOne
#include <eoSelectPerc.h>

9
eo/src/eoCombinedContinue.h
View file

@ -57,26 +57,35 @@ public:
{
}
/* FIXME remove in next release
/// Ctor - for historical reasons ... should disspear some day
eoCombinedContinue( eoContinue<EOT>& _cont1, eoContinue<EOT>& _cont2)
: eoContinue<EOT>(), std::vector<eoContinue<EOT>* >()
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The double continuators constructor of eocombinedContinue is deprecated and will be removed in the next release."
#endif // !DEPRECATED_MESSAGES
this->push_back(&_cont1);
this->push_back(&_cont2);
}
*/
void add(eoContinue<EOT> & _cont)
{
this->push_back(&_cont);
}
/* FIXME remove in next release
void removeLast(void)
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The removeLast method of eocombinedContinue is deprecated and will be removed in the next release, use pop_back instead."
#endif // !DEPRECATED_MESSAGES
this->pop_back();
}
*/
/** Returns false when one of the embedded continuators say so (logical and)

2
eo/src/eoCombinedInit.h
View file

@ -44,11 +44,13 @@ public:
rates.push_back(_rate);
}
/* FIXME remove in next release
void add(eoInit<EOT> & _init, double _rate, bool _verbose)
{
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoCombinedInit::add is deprecated and will be removed in the next release." << std::endl;
add( _init, _rate );
}
*/
/** The usual method to add objects to the combination
*/

2
eo/src/eoCtrlCContinue.h
View file

@ -30,7 +30,7 @@
#ifndef eoCtrlCContinue_h
#define eoCtrlCContinue_h
#include <signal.h>
#include <csignal>
#include <eoContinue.h>
/**

2
eo/src/eoDetSelect.h
View file

@ -34,7 +34,7 @@
#include <math.h>
//-----------------------------------------------------------------------------
/** eoDetSelect selects many individuals determinisctically
/** eoDetSelect selects many individuals deterministically
*
* @ingroup Selectors
*/

61
eo/src/eoEvalUserTimeThrowException.h
View file

@ -21,27 +21,30 @@ Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
#ifndef __unix__
#warning "Warning: class 'eoEvalUserTimeThrowException' is only available under UNIX systems (defining 'rusage' in 'sys/resource.h'), contributions for other systems are welcomed."
#else
#if !defined(__unix__) && !defined(_WINDOWS)
#warning "Warning: class 'eoEvalUserTimeThrowException' is only available under UNIX (defining 'rusage' in 'sys/resource.h') or Win32 (defining 'GetProcessTimes' in 'WinBase.h') systems, contributions for other systems are welcomed."
#else //!defined(__unix__) && !defined(_WINDOWS)
#ifndef __EOEVALUSERTIMETHROWEXCEPTION_H__
#define __EOEVALUSERTIMETHROWEXCEPTION_H__
#include <sys/time.h>
#include <sys/resource.h>
#include <eoExceptions.h>
/** Check at each evaluation if a given CPU user time contract has been reached.
*
* Throw an eoMaxTimeException if the given max time has been reached.
* Usefull if you want to end the search independently of generations.
* This class uses (almost-)POSIX headers.
* This class uses (almost-)POSIX or Win32 headers, depending on the platform.
* It uses a computation of the user time used on the CPU. For a wallclock time measure, see eoEvalTimeThrowException
*
* @ingroup Evaluation
*/
#include <eoExceptions.h>
#ifdef __unix__
#include <sys/time.h>
#include <sys/resource.h>
template< class EOT >
class eoEvalUserTimeThrowException : public eoEvalFuncCounter< EOT >
{
@ -58,7 +61,7 @@ public:
if( current >= _max ) {
throw eoMaxTimeException( current );
} else {
func(eo);
this->func(eo);
}
}
}
@ -68,5 +71,41 @@ protected:
struct rusage _usage;
};
#else
#ifdef _WINDOWS
//here _WINDOWS is defined
#include <WinBase.h>
template< class EOT >
class eoEvalUserTimeThrowException : public eoEvalFuncCounter< EOT >
{
public:
eoEvalUserTimeThrowException( eoEvalFunc<EOT> & func, const long max ) : eoEvalFuncCounter<EOT>( func, "CPU-user"), _max(max) {}
virtual void operator() ( EOT & eo )
{
if( eo.invalid() ) {
FILETIME dummy;
GetProcessTimes(GetCurrentProcess(), &dummy, &dummy, &dummy, &_usage);
ULARGE_INTEGER current;
current.LowPart = _usage.dwLowDateTime;
current.HighPart = _usage.dwHighDateTime;
if( current.QuadPart >= _max ) {
throw eoMaxTimeException( current.QuadPart );
} else {
func(eo);
}
}
}
protected:
const long _max;
FILETIME _usage;
};
#endif // _WINDOWS
#endif //__unix__
#endif // __EOEVALUSERTIMETHROWEXCEPTION_H__
#endif // __UNIX__
#endif //!defined(__unix__) && !defined(_WINDOWS)

11
eo/src/eoFunctorStore.h
View file

@ -28,6 +28,9 @@
#define _eoFunctorStore_h
#include <vector>
#include<algorithm>
#include "utils/eoLogger.h"
class eoFunctorBase;
@ -52,6 +55,13 @@ public:
template <class Functor>
Functor& storeFunctor(Functor* r)
{
#ifndef NDEBUG
unsigned int existing = std::count( vec.begin(), vec.end(), r );
if( existing > 0 ) {
eo::log << eo::warnings << "WARNING: you asked eoFunctorStore to store the functor " << r << " "
<< existing + 1 << " times, a segmentation fault may occur in the destructor." << std::endl;
}
#endif
// If the compiler complains about the following line,
// check if you really are giving it a pointer to an
// eoFunctorBase derived object
@ -67,6 +77,7 @@ private :
/** no assignment allowed */
eoFunctorStore operator=(const eoFunctorStore&);
protected:
std::vector<eoFunctorBase*> vec;
};

10
eo/src/eoMergeReduce.h
View file

@ -55,7 +55,7 @@ class eoMergeReduce : public eoReplacement<EOT>
merge(_merge), reduce(_reduce)
{}
void operator()(eoPop<EOT>& _parents, eoPop<EOT>& _offspring)
virtual void operator()(eoPop<EOT>& _parents, eoPop<EOT>& _offspring)
{
merge(_parents, _offspring); // parents untouched, result in offspring
reduce(_offspring, _parents.size());
@ -92,6 +92,14 @@ class eoCommaReplacement : public eoMergeReduce<EOT>
public :
eoCommaReplacement() : eoMergeReduce<EOT>(no_elite, truncate) {}
virtual void operator()(eoPop<EOT>& _parents, eoPop<EOT>& _offspring)
{
// There must be more offsprings than parents, or else an exception will be raised
assert( _offspring.size() >= _parents.size() );
eoMergeReduce<EOT>::operator()( _parents, _offspring );
}
private :
eoNoElitism<EOT> no_elite;
eoTruncate<EOT> truncate;

485
eo/src/eoPop.h
View file

@ -4,31 +4,41 @@
// eoPop.h
// (c) GeNeura Team, 1998
/*
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 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.
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
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
*/
Authors:
todos@geneura.ugr.es, http://geneura.ugr.es
jmerelo
gustavoromero
mac
maartenkeijzer
kuepper
okoenig
evomarc
Johann Dréo <johann.dreo@thalesgroup.com>
*/
//-----------------------------------------------------------------------------
#ifndef _EOPOP_H
#define _EOPOP_H
#ifndef _EOPOP_H_
#define _EOPOP_H_
#include <algorithm>
#include <iostream>
#include <iterator> // needed for GCC 3.2
#include <vector>
#include <assert.h>
// EO includes
#include <eoOp.h> // for eoInit
@ -54,18 +64,18 @@
template<class EOT>
class eoPop: public std::vector<EOT>, public eoObject, public eoPersistent
{
public:
public:
using std::vector<EOT>::size;
using std::vector<EOT>::resize;
using std::vector<EOT>::operator[];
using std::vector<EOT>::begin;
using std::vector<EOT>::end;
using std::vector<EOT>::size;
using std::vector<EOT>::resize;
using std::vector<EOT>::operator[];
using std::vector<EOT>::begin;
using std::vector<EOT>::end;
typedef typename EOT::Fitness Fitness;
typedef typename EOT::Fitness Fitness;
#if defined(__CUDACC__)
typedef typename std::vector<EOT>::iterator iterator;
typedef typename std::vector<EOT>::const_iterator const_iterator;
typedef typename std::vector<EOT>::iterator iterator;
typedef typename std::vector<EOT>::const_iterator const_iterator;
#endif
/** Default ctor. Creates empty pop
@ -74,268 +84,297 @@ public:
/** Ctor for the initialization of chromosomes
@param _popSize total population size
@param _chromInit Initialization routine, produces EO's, needs to be an eoInit
@param _popSize total population size
@param _chromInit Initialization routine, produces EO's, needs to be an eoInit
*/
eoPop( unsigned _popSize, eoInit<EOT>& _chromInit )
:std::vector<EOT>()
{
resize(_popSize);
for ( unsigned i = 0; i < _popSize; i++ )
{
eoPop( unsigned _popSize, eoInit<EOT>& _chromInit )
: std::vector<EOT>()
{
resize(_popSize);
for ( unsigned i = 0; i < _popSize; i++ )
{
_chromInit(operator[](i));
}
};
}
}
/** appends random guys at end of pop.
Can be used to initialize it pop is empty
Can be used to initialize it pop is empty
@param _newPopSize total population size
@param _chromInit Initialization routine, produces EO's, needs to be an eoInit
@param _newPopSize total population size
@param _chromInit Initialization routine, produces EO's, needs to be an eoInit
*/
void append( unsigned _newPopSize, eoInit<EOT>& _chromInit )
{
unsigned oldSize = size();
if (_newPopSize < oldSize)
void append( unsigned _newPopSize, eoInit<EOT>& _chromInit )
{
throw std::runtime_error("New size smaller than old size in pop.append");
return;
unsigned oldSize = size();
if (_newPopSize < oldSize)
{
throw std::runtime_error("New size smaller than old size in pop.append");
return;
}
if (_newPopSize == oldSize)
return;
resize(_newPopSize); // adjust the size
for ( unsigned i = oldSize; i < _newPopSize; i++ )
{
_chromInit(operator[](i));
}
}
if (_newPopSize == oldSize)
return;
resize(_newPopSize); // adjust the size
for ( unsigned i = oldSize; i < _newPopSize; i++ )
/** Ctor from an std::istream; reads the population from a stream,
each element should be in different lines
@param _is the stream
*/
eoPop( std::istream& _is ) :std::vector<EOT>()
{
_chromInit(operator[](i));
readFrom( _is );
}
};
/** Ctor from an std::istream; reads the population from a stream,
each element should be in different lines
@param _is the stream
*/
eoPop( std::istream& _is ) :std::vector<EOT>() {
readFrom( _is );
}
/** Empty Dtor */
/** Empty Dtor */
virtual ~eoPop() {}
/// helper struct for getting a pointer
struct Ref { const EOT* operator()(const EOT& eot) { return &eot;}};
/// helper struct for comparing on pointers
struct Cmp {
bool operator()(const EOT* a, const EOT* b) const
/// helper struct for getting a pointer
struct Ref { const EOT* operator()(const EOT& eot) { return &eot;}};
/// helper struct for comparing on pointers
struct Cmp {
bool operator()(const EOT* a, const EOT* b) const
{ return b->operator<(*a); }
};
/// helper struct for comparing (EA or PSO)
struct Cmp2
{
bool operator()(const EOT & a,const EOT & b) const
};
/// helper struct for comparing (EA or PSO)
struct Cmp2
{
bool operator()(const EOT & a,const EOT & b) const
{
return b.operator<(a);
}
};
/**
sort the population. Use this member to sort in order
of descending Fitness, so the first individual is the best!
*/
void sort(void)
{
std::sort(begin(), end(), Cmp2());
}
};
/** creates a std::vector<EOT*> pointing to the individuals in descending order */
void sort(std::vector<const EOT*>& result) const
{
result.resize(size());
/**
sort the population. Use this member to sort in order
of descending Fitness, so the first individual is the best!
*/
void sort(void)
{
std::sort(begin(), end(), Cmp2());
}
std::transform(begin(), end(), result.begin(), Ref());
/** creates a std::vector<EOT*> pointing to the individuals in descending order */
void sort(std::vector<const EOT*>& result) const
{
result.resize(size());
std::sort(result.begin(), result.end(), Cmp());
}
std::transform(begin(), end(), result.begin(), Ref());
std::sort(result.begin(), result.end(), Cmp());
}
/**
shuffle the population. Use this member to put the population
in random order
*/
void shuffle(void)
{
UF_random_generator<unsigned int> gen;
std::random_shuffle(begin(), end(), gen);
}
/**
shuffle the population. Use this member to put the population
in random order
*/
void shuffle(void)
{
UF_random_generator<unsigned int> gen;
std::random_shuffle(begin(), end(), gen);
}
/** creates a std::vector<EOT*> pointing to the individuals in random order */
void shuffle(std::vector<const EOT*>& result) const
{
result.resize(size());
/** creates a std::vector<EOT*> pointing to the individuals in random order */
void shuffle(std::vector<const EOT*>& result) const
{
result.resize(size());
std::transform(begin(), end(), result.begin(), Ref());
std::transform(begin(), end(), result.begin(), Ref());
UF_random_generator<unsigned int> gen;
std::random_shuffle(result.begin(), result.end(), gen);
}
UF_random_generator<unsigned int> gen;
std::random_shuffle(result.begin(), result.end(), gen);
}
/** returns an iterator to the best individual DOES NOT MOVE ANYBODY */
/** returns an iterator to the best individual DOES NOT MOVE ANYBODY */
#if defined(__CUDACC__)
eoPop<EOT>::iterator it_best_element()
{
eoPop<EOT>:: iterator it = std::max_element(begin(), end());
eoPop<EOT>::iterator it_best_element()
{
eoPop<EOT>:: iterator it = std::max_element(begin(), end());
#else
typename eoPop<EOT>::iterator it_best_element() {
typename eoPop<EOT>::iterator it = std::max_element(begin(), end());
typename eoPop<EOT>::iterator it_best_element()
{
assert( this->size() > 0 );
typename eoPop<EOT>::iterator it = std::max_element(begin(), end());
#endif
return it;
}
return it;
}
/** returns an iterator to the best individual DOES NOT MOVE ANYBODY */
const EOT & best_element() const
{
/** returns an iterator to the best individual DOES NOT MOVE ANYBODY */
const EOT & best_element() const
{
#if defined(__CUDACC__)
eoPop<EOT>::const_iterator it = std::max_element(begin(), end());
eoPop<EOT>::const_iterator it = std::max_element(begin(), end());
#else
typename eoPop<EOT>::const_iterator it = std::max_element(begin(), end());
typename eoPop<EOT>::const_iterator it = std::max_element(begin(), end());
#endif
if( it == end() )
throw std::runtime_error("eoPop<EOT>: Empty population, when calling best_element().");
return (*it);
}
if( it == end() )
throw std::runtime_error("eoPop<EOT>: Empty population, when calling best_element().");
return (*it);
}
/** returns a const reference to the worse individual DOES NOT MOVE ANYBODY */
const EOT & worse_element() const
{
/** returns a const reference to the worse individual DOES NOT MOVE ANYBODY */
const EOT & worse_element() const
{
#if defined(__CUDACC__)
eoPop<EOT>::const_iterator it = std::min_element(begin(), end());
eoPop<EOT>::const_iterator it = std::min_element(begin(), end());
#else
typename eoPop<EOT>::const_iterator it = std::min_element(begin(), end());
assert( this->size() > 0 );
typename eoPop<EOT>::const_iterator it = std::min_element(begin(), end());
#endif
return (*it);
}
return (*it);
}
/** returns an iterator to the worse individual DOES NOT MOVE ANYBODY */
/** returns an iterator to the worse individual DOES NOT MOVE ANYBODY */
#if defined(__CUDACC__)
eoPop<EOT>::iterator it_worse_element()
{
eoPop<EOT>::iterator it = std::min_element(begin(), end());
eoPop<EOT>::iterator it_worse_element()
{
eoPop<EOT>::iterator it = std::min_element(begin(), end());
#else
typename eoPop<EOT>::iterator it_worse_element()
{
typename eoPop<EOT>::iterator it = std::min_element(begin(), end());
typename eoPop<EOT>::iterator it_worse_element()
{
assert( this->size() > 0 );
typename eoPop<EOT>::iterator it = std::min_element(begin(), end());
#endif
return it;
}
return it;
}
/**
slightly faster algorithm than sort to find all individuals that are better
than the nth individual. INDIVIDUALS ARE MOVED AROUND in the pop.
*/
/**
slightly faster algorithm than sort to find all individuals that are better
than the nth individual. INDIVIDUALS ARE MOVED AROUND in the pop.
*/
#if defined(__CUDACC__)
eoPop<EOT>::iterator nth_element(int nth)
{
eoPop<EOT>::iterator it = begin() + nth;
eoPop<EOT>::iterator nth_element(int nth)
{
eoPop<EOT>::iterator it = begin() + nth;
#else
typename eoPop<EOT>::iterator nth_element(int nth)
{
typename eoPop<EOT>::iterator it = begin() + nth;
typename eoPop<EOT>::iterator nth_element(int nth)
{
assert( this->size() > 0 );
typename eoPop<EOT>::iterator it = begin() + nth;
#endif
std::nth_element(begin(), it, end(), std::greater<EOT>());
return it;
}
std::nth_element(begin(), it, end(), std::greater<EOT>());
return it;
}
struct GetFitness { Fitness operator()(const EOT& _eo) const { return _eo.fitness(); } };
/** returns the fitness of the nth element */
Fitness nth_element_fitness(int which) const
{ // probably not the fastest way to do this, but what the heck
struct GetFitness { Fitness operator()(const EOT& _eo) const { return _eo.fitness(); } };
std::vector<Fitness> fitness(size());
std::transform(begin(), end(), fitness.begin(), GetFitness());
typename std::vector<Fitness>::iterator it = fitness.begin() + which;
std::nth_element(fitness.begin(), it, fitness.end(), std::greater<Fitness>());
return *it;
}
/** returns the fitness of the nth element */
Fitness nth_element_fitness(int which) const
{ // probably not the fastest way to do this, but what the heck
/** const nth_element function, returns pointers to sorted individuals
* up the the nth
*/
void nth_element(int which, std::vector<const EOT*>& result) const
{
std::vector<Fitness> fitness(size());
std::transform(begin(), end(), fitness.begin(), GetFitness());
result.resize(size());
std::transform(begin(), end(), result.begin(), Ref());
typename std::vector<Fitness>::iterator it = fitness.begin() + which;
std::nth_element(fitness.begin(), it, fitness.end(), std::greater<Fitness>());
return *it;
}
typename std::vector<const EOT*>::iterator it = result.begin() + which;
std::nth_element(result.begin(), it, result.end(), Cmp());
}
/** const nth_element function, returns pointers to sorted individuals
* up the the nth
*/
void nth_element(int which, std::vector<const EOT*>& result) const
{
/** does STL swap with other pop */
void swap(eoPop<EOT>& other)
{
std::swap(static_cast<std::vector<EOT>& >(*this), static_cast<std::vector<EOT>& >(other));
}
assert( this->size() > 0 );
result.resize(size());
std::transform(begin(), end(), result.begin(), Ref());
/**
* Prints sorted pop but does NOT modify it!
*
* @param _os A std::ostream.
*/
virtual void sortedPrintOn(std::ostream& _os) const
{
std::vector<const EOT*> result;
sort(result);
_os << size() << '\n';
for (unsigned i = 0; i < size(); ++i)
{
_os << *result[i] << std::endl;
}
}
typename std::vector<const EOT*>::iterator it = result.begin() + which;
/**
* Write object. It's called printOn since it prints the object _on_ a stream.
* @param _os A std::ostream.
*/
virtual void printOn(std::ostream& _os) const
{
_os << size() << '\n';
std::copy( begin(), end(), std::ostream_iterator<EOT>( _os, "\n") );
}
std::nth_element(result.begin(), it, result.end(), Cmp());
}
/** @name Methods from eoObject */
//@{
/**
* Read object. The EOT class must have a ctor from a stream;
* @param _is A std::istream.
*/
virtual void readFrom(std::istream& _is)
{
size_t sz;
_is >> sz;
resize(sz);
/** does STL swap with other pop */
void swap(eoPop<EOT>& other)
{
std::swap(static_cast<std::vector<EOT>& >(*this), static_cast<std::vector<EOT>& >(other));
}
for (size_t i = 0; i < sz; ++i) {
operator[](i).readFrom( _is );
}
}
/** Inherited from eoObject. Returns the class name.
@see eoObject
*/
virtual std::string className() const {return "eoPop";};
//@}
/**
* Prints sorted pop but does NOT modify it!
*
* @param _os A std::ostream.
*/
virtual void sortedPrintOn(std::ostream& _os) const
{
std::vector<const EOT*> result;
sort(result);
_os << size() << '\n';
for (unsigned i = 0; i < size(); ++i)
{
_os << *result[i] << std::endl;
}
}
virtual void invalidate()
{
for (unsigned i=0; i<size(); i++)
this->operator[](i).invalidate();
}
};
#endif
/**
* Write object. It's called printOn since it prints the object _on_ a stream.
* @param _os A std::ostream.
*/
virtual void printOn(std::ostream& _os) const
{
_os << size() << '\n';
std::copy( begin(), end(), std::ostream_iterator<EOT>( _os, "\n") );
}
/** @name Methods from eoObject */
//@{
/**
* Read object. The EOT class must have a ctor from a stream;
* @param _is A std::istream.
*/
virtual void readFrom(std::istream& _is)
{
size_t sz;
_is >> sz;
resize(sz);
for (size_t i = 0; i < sz; ++i) {
operator[](i).readFrom( _is );
}
}
/** Inherited from eoObject. Returns the class name.
@see eoObject
*/
virtual std::string className() const {return "eoPop";};
//@}
/** Invalidate the whole population
*/
virtual void invalidate()
{
for (unsigned i=0; i<size(); i++)
this->operator[](i).invalidate();
}
}; // class eoPop
#endif // _EOPOP_H_

7
eo/src/eoProportionalCombinedOp.h
View file

@ -186,12 +186,17 @@ public:
virtual std::string className() const { return "eoPropCombinedQuadOp"; }
/* FIXME remove in next release
virtual void add(eoQuadOp<EOT> & _op, const double _rate, bool _verbose)
{
#ifndef DEPRECATED_MESSAGES
#pragma message "The use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release."
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoPropCombinedQuadOp::add is deprecated and will be removed in the next release." << std::endl;
#endif // !DEPRECATED_MESSAGES
add(_op,_rate);
}
*/
// addition of a true operator
virtual void add(eoQuadOp<EOT> & _op, const double _rate)
@ -199,7 +204,7 @@ public:
ops.push_back(&_op);
rates.push_back(_rate);
// compute the relative rates in percent - to warn the user!
printOn( eo::log << eo::logging );
printOn( eo::log << eo::logging );
}
// outputs the operators and percentages

54
eo/src/eoRankMuSelect.h Normal file
View file

@ -0,0 +1,54 @@
/*
The Evolving Distribution Objects framework (EDO) is a template-based,
ANSI-C++ evolutionary computation library which helps you to write your
own estimation of distribution algorithms.
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 2.1 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Copyright (C) 2012 Thales group
*/
/*
Authors:
Johann Dréo <johann.dreo@thalesgroup.com>
*/
#ifndef _eoRankMuSelect_h
#define _eoRankMuSelect_h
#include "eoDetSelect.h"
/** Selects the "Mu" bests individuals.
*
* Note: sorts the population before trucating it.
*
* @ingroup Selectors
*/
template<typename EOT>
class eoRankMuSelect : public eoDetSelect<EOT>
{
public :
// false, because mu is not a rate
eoRankMuSelect( unsigned int mu ) : eoDetSelect<EOT>( mu, false ) {}
void operator()(const eoPop<EOT>& source, eoPop<EOT>& dest)
{
eoPop<EOT> tmp( source );
tmp.sort();
eoDetSelect<EOT>::operator()( tmp, dest );
}
};
#endif // !_eoRankMuselect_h

2
eo/src/eoReduceSplit.h
View file

@ -104,7 +104,7 @@ public:
unsigned eliminated = howMany(popSize);
if (!eliminated) // nothing to do
return ;
unsigned newsize = popSize - eliminated;
long newsize = static_cast<long>(popSize) - static_cast<long>(eliminated);
if (newsize < 0)
throw std::logic_error("eoLinearTruncateSplit: Cannot truncate to a larger size!\n");

2
eo/src/eoScalarFitnessAssembled.h
View file

@ -212,7 +212,7 @@ public:
//! Print term values and descriptions
void printAll(std::ostream& os) const {
for (size_type i=0; i < size(); ++i )
os << FitnessTraits::getDescription(i) << " = " << operator[](i) << " ";
os << FitnessTraits::getDescription(i) << " = " << this->operator[](i) << " ";
}
//! Comparison, using less by default

58
eo/src/ga/eoBitOp.h
View file

@ -56,7 +56,7 @@ template<class Chrom> class eoOneBitFlip: public eoMonOp<Chrom>
bool operator()(Chrom& chrom)
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
chrom[i] = !chrom[i];
return true;
}
};
@ -85,11 +85,11 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
*/
bool operator()(Chrom& chrom)
{
// does not check for duplicate: if someone volunteers ....
// for duplicate checking see eoDetSingleBitFlip
for (unsigned k=0; k<num_bit; k++)
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
chrom[i] = !chrom[i];
}
return true;
}
@ -98,6 +98,58 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
};
/** eoDetSingleBitFlip --> changes exactly k bits with checking for duplicate
\class eoDetSingleBitFlip eoBitOp.h ga/eoBitOp.h
\ingroup bitstring
*/
template<class Chrom> class eoDetSingleBitFlip: public eoMonOp<Chrom>
{
public:
/**
* (Default) Constructor.
* @param _num_bit The number of bits to change
* default is one - equivalent to eoOneBitFlip then
*/
eoDetSingleBitFlip(const unsigned& _num_bit = 1): num_bit(_num_bit) {}
/// The class name.
virtual std::string className() const { return "eoDetSingleBitFlip"; }
/**
* Change num_bit bits.
* @param chrom The cromosome which one bit is going to be changed.
*/
bool operator()(Chrom& chrom)
{
std::vector< unsigned > selected;
// check for duplicate
for (unsigned k=0; k<num_bit; k++)
{
unsigned temp;
do
{
temp = eo::rng.random( chrom.size() );
}
while ( find( selected.begin(), selected.end(), temp ) != selected.end() );
selected.push_back(temp);
}
for ( size_t i = 0; i < selected.size(); ++i )
{
chrom[i] = !chrom[i];
}
return true;
}
private:
unsigned num_bit;
};
/** eoBitMutation --> classical mutation
\class eoBitMutation eoBitOp.h ga/eoBitOp.h
\ingroup bitstring

2
eo/src/ga/make_continue_ga.cpp
View file

@ -37,7 +37,7 @@
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h
* while the TEMPLATIZED code is define in make_contninue.h in the src/do dir
* while the TEMPLATIZED code is define in make_continue.h in the src/do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations

4
eo/src/ga/make_ga.h
View file

@ -57,8 +57,8 @@
*/
// the genotypes
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo);
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo);
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias=0.5);
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias=0.5);
// the operators
eoGenOp<eoBit<double> >& make_op(eoParser& _parser, eoState& _state, eoInit<eoBit<double> >& _init);

8
eo/src/ga/make_genotype_ga.cpp
View file

@ -45,11 +45,11 @@
/// The following function merely call the templatized do_* functions above
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo)
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo, float _bias)
{
return do_make_genotype(_parser, _state, _eo);
return do_make_genotype(_parser, _state, _eo, _bias);
}
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo)
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo, float _bias)
{
return do_make_genotype(_parser, _state, _eo);
return do_make_genotype(_parser, _state, _eo, _bias);
}

4
eo/src/ga/make_genotype_ga.h
View file

@ -60,7 +60,7 @@
* @ingroup Builders
*/
template <class EOT>
eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT, float _bias=0.5)
{
// for bitstring, only thing needed is the size
// but it might have been already read in the definition fo the performance
@ -68,7 +68,7 @@ eoInit<EOT> & do_make_genotype(eoParser& _parser, eoState& _state, EOT)
// Then we can built a bitstring random initializer
// based on boolean_generator class (see utils/rnd_generator.h)
eoBooleanGenerator * gen = new eoBooleanGenerator;
eoBooleanGenerator * gen = new eoBooleanGenerator(_bias);
_state.storeFunctor(gen);
eoInitFixedLength<EOT>* init = new eoInitFixedLength<EOT>(theSize, *gen);
// store in state

25
eo/src/ga/make_op.h
View file

@ -115,11 +115,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
throw std::runtime_error("Invalid uRate");
// minimum check
bool bCross = true;
// bool bCross = true; // not used ?
if (onePointRateParam.value()+twoPointsRateParam.value()+uRateParam.value()==0)
{
std::cerr << "Warning: no crossover" << std::endl;
bCross = false;
// bCross = false;
}
// Create the CombinedQuadOp
@ -156,17 +156,29 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
if ( (bitFlipRateParam.value() < 0) )
throw std::runtime_error("Invalid bitFlipRate");
// oneBitFlip
eoValueParam<double> & oneBitRateParam = _parser.createParam(0.01, "oneBitRate", "Relative rate for deterministic bit-flip mutation", 'd', "Variation Operators" );
// minimum check
if ( (oneBitRateParam.value() < 0) )
throw std::runtime_error("Invalid oneBitRate");
// kBitFlip
eoValueParam<unsigned> & kBitParam = _parser.createParam((unsigned)1, "kBit", "Number of bit for deterministic k bit-flip mutation", 0, "Variation Operators" );
// minimum check
bool bMut = true;
if ( ! kBitParam.value() )
throw std::runtime_error("Invalid kBit");
eoValueParam<double> & kBitRateParam = _parser.createParam(0.0, "kBitRate", "Relative rate for deterministic k bit-flip mutation", 0, "Variation Operators" );
// minimum check
if ( (kBitRateParam.value() < 0) )
throw std::runtime_error("Invalid kBitRate");
// minimum check
// bool bMut = true; // not used ?
if (bitFlipRateParam.value()+oneBitRateParam.value()==0)
{
std::cerr << "Warning: no mutation" << std::endl;
bMut = false;
// bMut = false;
}
// Create the CombinedMonOp
@ -184,6 +196,11 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
_state.storeFunctor(ptMon);
ptCombinedMonOp->add(*ptMon, oneBitRateParam.value());
// mutate exactly k bit per individual
ptMon = new eoDetBitFlip<EOT>(kBitParam.value());
_state.storeFunctor(ptMon);
ptCombinedMonOp->add(*ptMon, kBitRateParam.value());
_state.storeFunctor(ptCombinedMonOp);
// now build the eoGenOp:

4
eo/src/gp/eoParseTree.h
View file

@ -94,7 +94,7 @@ public:
while (size() > _size)
{
back() = operator[](size()-2);
back() = this->operator[](size()-2);
}
}
@ -150,7 +150,7 @@ public:
v[i] = node;
}
parse_tree<Node> tmp(v.begin(), v.end());
swap(tmp);
this->swap(tmp);
/*
* old code which caused problems for paradisEO

2
eo/src/pyeo/test/run_tests.sh
View file

@ -2,6 +2,6 @@
for i in *.py
do
python $i > /dev/null
python2 $i > /dev/null
done

1
eo/src/utils/CMakeLists.txt
View file

@ -29,6 +29,7 @@ SET(EOUTILS_SOURCES
pipecom.cpp
eoLogger.cpp
eoParallel.cpp
eoSignal.cpp
)
ADD_LIBRARY(eoutils STATIC ${EOUTILS_SOURCES})

33
eo/src/utils/checkpointing
View file

@ -1,3 +1,29 @@
/*
-----------------------------------------------------------------------------
checkpointing
(c) Maarten Keijzer (mak@dhi.dk) and GeNeura Team, 1999, 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
*/
#ifndef _CHECKPOINTING_
#define _CHECKPOINTING_
#include <utils/eoParser.h>
#include <utils/eoState.h>
#include <utils/eoUpdater.h>
@ -10,6 +36,7 @@
#include <utils/eoGnuplot1DSnapshot.h>
#endif
#include <utils/eoCheckPoint.h>
#include <utils/eoSignal.h>
#include <utils/eoStat.h>
#include <utils/eoScalarFitnessStat.h>
#include <utils/eoAssembledFitnessStat.h>
@ -21,3 +48,9 @@
// and make_help - any better suggestion to include it?
void make_help(eoParser & _parser);
#endif // !_CHECKPOINTING_
// Local Variables:
// mode: C++
// End:

36
eo/src/utils/eoFuncPtrStat.h
View file

@ -4,6 +4,8 @@
#include <eoFunctorStore.h>
#include <utils/eoStat.h>
/** Wrapper to turn any stand-alone function and into an eoStat.
*
* The function should take an eoPop as argument.
@ -41,4 +43,38 @@ eoFuncPtrStat<EOT, T>& makeFuncPtrStat( T (*func)(const eoPop<EOT>&), eoFunctorS
);
}
/** Wrapper to turn any stand-alone function and into an eoStat.
*
* The function should take an eoPop as argument.
*
* @ingroup Stats
*/
template <class EOT, class T>
class eoFunctorStat : public eoStat<EOT, T>
{
public :
eoFunctorStat(eoUF< const eoPop<EOT>&, T >& f, std::string _description = "functor")
: eoStat<EOT, T>(T(), _description), func(f)
{}
using eoStat<EOT, T>::value;
void operator()(const eoPop<EOT>& pop) {
value() = func(pop);
}
private:
eoUF< const eoPop<EOT>&, T >& func;
};
/**
* @ingroup Stats
*/
template <class EOT, class T>
eoFunctorStat<EOT, T>& makeFunctorStat( eoUF< const eoPop<EOT>&, T >& func, eoFunctorStore& store, std::string description = "func") {
return store.storeFunctor(
new eoFunctorStat<EOT, T>( func, description)
);
}
#endif

3
eo/src/utils/eoLogger.cpp
View file

@ -194,8 +194,7 @@ int eoLogger::outbuf::overflow(int_type c)
{
if (_fd >= 0 && c != EOF)
{
size_t num;
num = ::write(_fd, &c, 1);
::write(_fd, &c, 1);
}
}
return c;

1
eo/src/utils/eoOStreamMonitor.cpp
View file

@ -37,6 +37,7 @@ eoMonitor& eoOStreamMonitor::operator()(void)
} // if firstime
// ok, now the real saving. write out
// FIXME deprecated, remove in next release
//! @todo old verbose formatting, do we still need it?
/*
for (iterator it = vec.begin (); it != vec.end (); ++it) {

6
eo/src/utils/eoOStreamMonitor.h
View file

@ -44,13 +44,17 @@ Authors:
class eoOStreamMonitor : public eoMonitor
{
public :
/* FIXME remove in next release
eoOStreamMonitor( std::ostream & _out, bool _verbose=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
out(_out), delim(_delim), width(_width), fill(_fill), firsttime(true)
{
(void)_verbose;
#ifndef DEPRECATED_MESSAGES
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#pragma message "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release"
#endif // !DEPRECATED_MESSAGES
}
*/
eoOStreamMonitor( std::ostream & _out, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
out(_out), delim(_delim), width(_width), fill(_fill), firsttime(true)

2
eo/src/utils/eoParallel.cpp
View file

@ -25,7 +25,9 @@ Authors:
*/
#ifdef _OPENMP
#include <omp.h>
#endif
#include "eoParallel.h"
#include "eoLogger.h"

36
eo/src/utils/eoParserLogger.h
View file

@ -1,36 +0,0 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/*
(c) Thales group, 2010
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;
version 2 of the License.
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: http://eodev.sourceforge.net
Authors:
Caner Candan <caner.candan@thalesgroup.com>
*/
#ifndef EO_PARSER_LOGGER_H
#define EO_PARSER_LOGGER_H
#include "eoParser.h"
#warning "[eoParserLogger] is deprecated"
typedef eoParser eoParserLogger;
#endif // !EO_PARSER_LOGGER_H

6
eo/src/utils/eoRNG.h
View file

@ -150,7 +150,8 @@ public :
initialize(2*s);
}
/** Re-initializes the Random Number Generator
/* FIXME remove in next release
** Re-initializes the Random Number Generator
This is the traditional seeding procedure. This version is deprecated and
only provided for compatibility with old code. In new projects you should
@ -159,11 +160,12 @@ public :
@see reseed for details on usage of the seeding value.
@version old version (deprecated)
*/
*
void oldReseed(uint32_t s)
{
initialize(s);
}
*/
/** Random number from unifom distribution

36
eo/src/utils/eoSignal.cpp Normal file
View file

@ -0,0 +1,36 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/**
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: http://eodev.sourceforge.net
Autors: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
Caner.Candan@univ-angers.fr
*/
#include <utils/eoSignal.h>
/**
* @addtogroup Continuators
* @{
*/
// --- Global variables - but don't know what else to do - MS ---
std::map< int, bool > signals_called;
/** @} */

106
eo/src/utils/eoSignal.h Normal file
View file

@ -0,0 +1,106 @@
// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
/**
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: http://eodev.sourceforge.net
Authors: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
Caner.Candan@univ-angers.fr
*/
#ifndef _eoSignal_h
#define _eoSignal_h
#include <csignal>
#include <utils/eoCheckPoint.h>
#include <utils/eoLogger.h>
#include <map>
#include <vector>
/**
* @addtogroup Continuators
* @{
*/
extern std::map< int, bool > signals_called;
/** eoSignal inherits from eoCheckPoint including signals handling (see signal(7))
*
* @ingroup Utilities
*/
template <class EOT>
class eoSignal : public eoCheckPoint<EOT>
{
public :
eoSignal( int sig = SIGINT ) : eoCheckPoint<EOT>( _dummyContinue ), _sig( sig )
{
::signals_called[_sig] = false;
#ifndef _WINDOWS
#ifdef SIGQUIT
::signal( _sig, handler );
#endif // !SIGQUIT
#endif // !_WINDOWS
}
eoSignal( eoContinue<EOT>& _cont, int sig = SIGINT ) : eoCheckPoint<EOT>( _cont ), _sig( sig )
{
::signals_called[_sig] = false;
#ifndef _WINDOWS
#ifdef SIGQUIT
::signal( _sig, handler );
#endif // !SIGQUIT
#endif // !_WINDOWS
}
bool operator()( const eoPop<EOT>& _pop )
{
bool& called = ::signals_called[_sig];
if ( called )
{
eo::log << eo::logging << "Signal granted…" << std::endl ;
called = false;
return this->eoCheckPoint<EOT>::operator()( _pop );
}
return true;
}
virtual std::string className(void) const { return "eoSignal"; }
static void handler( int sig )
{
::signals_called[sig] = true;
eo::log << eo::logging << "Signal wished…" << std::endl ;
}
private:
class DummyContinue : public eoContinue<EOT>
{
public:
bool operator() ( const eoPop<EOT>& ) { return true; }
} _dummyContinue;
int _sig;
};
/** @} */
#endif // !_eoSignal_h

62
eo/src/utils/eoState.cpp
View file

@ -18,7 +18,7 @@ using namespace std;
void removeComment(string& str, string comment)
void eoState::removeComment(string& str, string comment)
{
string::size_type pos = str.find(comment);
@ -28,21 +28,23 @@ void removeComment(string& str, string comment)
}
}
bool is_section(const string& str, string& name)
bool eoState::is_section(const string& str, string& name)
{
string::size_type pos = str.find("\\section{");
string::size_type pos = str.find(_tag_section_so);
if (pos == string::npos)
return false;
//else
string::size_type end = str.find("}");
string::size_type end = str.find(_tag_section_sc);
if (end == string::npos)
return false;
// else
name = str.substr(pos + 9, end-9);
// affect name, passed by reference
// Note: substr( start, count )
name = str.substr( pos + _tag_section_so.size(), end - _tag_section_so.size() );
return true;
}
@ -84,6 +86,7 @@ void eoState::load(const string& _filename)
load(is);
}
// FIXME implement parsing and loading of other formats
void eoState::load(std::istream& is)
{
string str;
@ -158,16 +161,49 @@ void eoState::save(const string& filename) const
save(os);
}
void eoState::save(std::ostream& os) const
{ // saves in order of insertion
for (vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin(); it != creationOrder.end(); ++it)
{
os << "\\section{" << (*it)->first << "}\n";
(*it)->second->printOn(os);
os << '\n';
}
//void eoState::save(std::ostream& os) const
//{ // saves in order of insertion
// for (vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin(); it != creationOrder.end(); ++it)
// {
// os << "\\section{" << (*it)->first << "}\n";
// (*it)->second->printOn(os);
// os << '\n';
// }
//}
void eoState::saveSection( std::ostream& os, vector<ObjectMap::iterator>::const_iterator it) const
{
os << _tag_section_so << (*it)->first << _tag_section_sc;
os << _tag_content_s;
(*it)->second->printOn(os);
os << _tag_content_e;
os << _tag_section_e;
}
void eoState::save(std::ostream& os) const
{
os << _tag_state_so << _tag_state_name << _tag_state_sc;
// save the first section
assert( creationOrder.size() > 0 );
// saves in order of insertion
vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin();
saveSection(os,it);
it++;
while( it != creationOrder.end() ) {
// add a separator only before [1,n] elements
os << _tag_section_sep;
saveSection(os, it);
it++;
}
os << _tag_state_e;
}
string eoState::createObjectName(eoObject* obj)
{
if (obj == 0)

80
eo/src/utils/eoState.h
View file

@ -31,6 +31,7 @@
#include <string>
#include <map>
#include <vector>
#include <assert.h>
#include <eoFunctorStore.h>
@ -56,10 +57,50 @@ class eoState : public eoFunctorStore
{
public :
eoState(void) {}
eoState(std::string name="") :
_tag_state_so(""),
_tag_state_name(name),
_tag_state_sc(""),
_tag_section_so("\\section{"),
_tag_section_sc("}\n"),
_tag_content_s(""),
_tag_content_e(""),
_tag_section_sep(""),
_tag_section_e("\n"),
_tag_state_e("")
{}
~eoState(void);
void formatLatex(std::string name)
{
_tag_state_so = "";
_tag_state_name = name;
_tag_state_sc = "";
_tag_section_so = "\\section{";
_tag_section_sc = "}\n";
_tag_content_s = "";
_tag_content_e = "";
_tag_section_sep = "";
_tag_section_e = "\n";
_tag_state_e = "";
}
void formatJSON(std::string name)
{
_tag_state_so = "{ \"";
_tag_state_name = name;
_tag_state_sc = "\":\n";
_tag_section_so = "\t{ \"";
_tag_section_sc = "\":\n";
_tag_content_s = "\"";
_tag_content_e = "\"";
_tag_section_sep = ",\n";
_tag_section_e = "\t}\n";
_tag_state_e = "}\n";
}
/**
* Object registration function, note that it does not take ownership!
*/
@ -131,6 +172,43 @@ private :
eoState(const eoState&);
eoState& operator=(const eoState&);
/* \@{
* s=start, e=end
* o=open, c=close
*
* { "my_state":
* {
* "section_pop":"…",
* "section_rng":"…"
* }
* }
*
* // JSON LATEX (default)
*/
std::string _tag_state_so; // { "
std::string _tag_state_name; // my_state
std::string _tag_state_sc; // ":
std::string _tag_section_so; // { " \\section{
std::string _tag_section_sc; // ": }\n
std::string _tag_content_s; // "
std::string _tag_content_e; // "
std::string _tag_section_sep;// ,
std::string _tag_section_e; // } \n
std::string _tag_state_e; // }
/** \@} */
void removeComment( std::string& str, std::string comment);
bool is_section(const std::string& str, std::string& name);
protected:
void saveSection( std::ostream& os, std::vector<ObjectMap::iterator>::const_iterator it) const;
};
/** @example t-eoStateAndParser.cpp
*/

6
eo/src/utils/eoStdoutMonitor.h
View file

@ -43,11 +43,15 @@ Authors:
class eoStdoutMonitor : public eoOStreamMonitor
{
public :
/* FIXME remove in next release
eoStdoutMonitor(bool _verbose, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
eoOStreamMonitor( std::cout, _verbose, _delim, _width, _fill)
{
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#ifndef DEPRECATED_MESSAGES
eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoStdoutMonitor constructor is deprecated and will be removed in the next release" << std::endl;
#endif // !DEPRECATED_MESSAGES
}
*/
eoStdoutMonitor(std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) :
eoOStreamMonitor( std::cout, _delim, _width, _fill)

2
eo/test/CMakeLists.txt
View file

@ -26,7 +26,7 @@ LINK_DIRECTORIES(${EO_BINARY_DIR}/lib)
IF(WITH_MPI)
LINK_DIRECTORIES(${MPI_DIR}/lib)
SET(CMAKE_CXX_COMPILER "${MPI_DIR}/bin/mpicxx")
SET(CMAKE_CXX_COMPILER "mpicxx")
ENDIF()
######################################################################################

2
eo/test/mpi/CMakeLists.txt
View file

@ -38,7 +38,7 @@ FOREACH (test ${TEST_LIST})
SET ("T_${test}_SOURCES" "${test}.cpp")
ENDFOREACH (test)
SET(CMAKE_CXX_COMPILER "${MPI_DIR}/bin/mpicxx")
SET(CMAKE_CXX_COMPILER "mpicxx")
ADD_DEFINITIONS(-DWITH_MPI)
IF(ENABLE_CMAKE_TESTING)

3
eo/test/t-MGE-control.cpp
View file

@ -69,7 +69,8 @@ int main()
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2 );
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);

3
eo/test/t-MGE.cpp
View file

@ -73,7 +73,8 @@ int main()
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);

3
eo/test/t-MGE1bit.cpp
View file

@ -72,7 +72,8 @@ int main()
// Terminators
eoGenContinue<Chrom> continuator1(10);
eoFitContinue<Chrom> continuator2(CHROM_SIZE);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add(continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);

3
eo/test/t-eobin.cpp
View file

@ -139,7 +139,8 @@ void main_function()
eoGenContinue<Chrom> continuator1(50);
eoFitContinue<Chrom> continuator2(65535.f);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCombinedContinue<Chrom> continuator(continuator1);
continuator.add( continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);

2
eo/test/t-openmp.cpp
View file

@ -39,6 +39,8 @@ Caner Candan <caner.candan@thalesgroup.com>
#include <omp.h>
#include <unistd.h>
#include "real_value.h"
//-----------------------------------------------------------------------------