bool CursorSelectTool::selectDeme(const QPoint& mousePos)
{
QList<QPoint> &selection = m_mapWidget->selection();
Deme *deme = m_mapWidget->map()->deme(mousePos.x() / m_mapWidget->demeSize(),
mousePos.y() / m_mapWidget->demeSize());
// Check if the mouse was over the map
if (deme == nullptr)
{
return false;
}
QPoint demeCoord(deme->x(), deme->y());
// If the user is selecting, the deme coordinate is added to the selection if it's not already in it.
if (m_selecting)
{
if (! selection.contains(demeCoord))
{
selection << demeCoord;
return true;
}
}
else // Else, the deme coordinate is removed from the selection
{
if (selection.contains(demeCoord))
{
selection.removeOne(demeCoord);
return true;
}
}
return false;
}
/*!
* \brief Apply the characteristic operation.
* \param ioDeme Deme to use to write the milestone.
* \param ioContext Context of the evolution.
*/
void RandomShuffleDemeOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::random_shuffle(ioDeme.begin(), ioDeme.end(),
ioContext.getSystem().getRandomizer());
Beagle_StackTraceEndM("void RandomShuffleDemeOp::operate(Deme& ioDeme, Context& ioContext)");
}
void LogIndividualDataOp::operate(Deme& ioDeme, Context& ioContext) {
Beagle_StackTraceBeginM();
if(mNumberIndividualPerDem->getWrappedValue() <= 0) {
return;
}
// Temporary buffer of individuals.
Individual::Bag lTempPop;
if(ioContext.getGeneration() != mGenerationCalculated) {
mGenerationCalculated = ioContext.getGeneration();
mNbDemesCalculated = 0;
}
if(++mNbDemesCalculated == mPopSize->size() && mOnlyVivarium->getWrappedValue()) {
//Make heap of all individual in the vivarium
for( unsigned int i = 0; i < ioContext.getVivarium().size(); ++i) {
lTempPop.insert(lTempPop.end(), ioContext.getVivarium()[i]->begin(), ioContext.getVivarium()[i]->end());
}
} else if(mOnlyVivarium->getWrappedValue()){
return;
} else {
//Process only this deme
// Insert pointer of all the individuals of the deme in the buffer.
lTempPop.insert(lTempPop.end(), ioDeme.begin(), ioDeme.end());
}
// Make the buffer a STL heap with the fittest individual on the top.
std::make_heap(lTempPop.begin(), lTempPop.end(), IsLessPointerPredicate());
for(unsigned int i = 0; i < mNumberIndividualPerDem->getWrappedValue(); ++i) {
Individual::Handle lIndividual = NULL;
if( !mKeepData->getWrappedValue() ) {
//Strip the simulation data of the individual
lIndividual = castHandleT<Individual>(ioDeme.getTypeAlloc()->cloneData(*lTempPop[0]));
LogFitness::Handle lFitness = castHandleT<LogFitness>(lIndividual->getFitness());
lFitness->clearData();
} else {
lIndividual = lTempPop[0];
}
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eStats,
"history", "Beagle::LogIndividualDataOp",
*lIndividual
);
// STL heap pop of the best individual of the temporary buffer.
std::pop_heap(lTempPop.begin(), lTempPop.end(), IsLessPointerPredicate());
lTempPop.pop_back();
}
Beagle_StackTraceEndM("void LogIndividualDataOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Distribute groups of individuals to evaluators nodes childs.
* \param ioDeme Current deme to execute the operator.
* \param ioContext Current context to execute the operator.
* This function distributed individuals to the evolver's evaluators.
*
* It first checks if the deme has a \ref ProcessingBuffer. The buffer
* is used to memorize which individuals had invalid fitness, since the
* function only distributes individuals that were modified during the
* current generation. Once the buffer is filled, the individuals are
* distributed to evaluator.
* The number of individuals an evaluato will received is based on this
* formula :
* \f[ NbIndividuals =
\left\{
\begin{array}{lr}
\frac{BufferSize}{NbEvaluators} + 1, & EvaluatorRank > BufferSize \pmod{NbEvaluators} \\
\frac{BufferSize}{NbEvaluators}, & else
\end{array}
\right.
\f]
*
* The function write the individuals in a streamer. The streamer opening
* tag is <Population> so the evaluator can directly read the string at
* its reception as a deme.
*
* The string are sent using a non-blocking send function, so the function
* doesn't have to wait for the transaction to be completed before starting
* to build another packet of individuals. The function ends when all
* packets have been sent.
*/
void HPC::DistributeDemeToEvaluatorsOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
unsigned int lNbEvaluators = mComm->getNbrOfRelation("Child");
ProcessingBuffer::Handle lBuffer = castHandleT<ProcessingBuffer>(ioDeme.getMember("ProcessingBuffer"));
if(lBuffer==0){
lBuffer = new ProcessingBuffer;
ioDeme.addMember(lBuffer);
}
lBuffer->clear();
for(unsigned int i = 0; i < ioDeme.size(); ++i){
if((ioDeme[i]->getFitness() == 0) ||
(ioDeme[i]->getFitness()->isValid() == false)){
lBuffer->push_back(ioDeme[i], i);
}
}
unsigned int lNbIndividualInt = lBuffer->size() / lNbEvaluators;
unsigned int lNbIndividualFrac = lBuffer->size() % lNbEvaluators;
unsigned int lNbIndividualTotal = 0;
unsigned int lNbIndividual = 0;
std::vector<std::string> lStreams(lNbEvaluators);
MPICommunication::Request::Bag lRequests(lNbEvaluators);
for(unsigned int i = 0; i < lNbEvaluators; ++i){
lNbIndividual = lNbIndividualInt;
if(i < lNbIndividualFrac)
lNbIndividual++;
std::ostringstream lOutStream;
PACC::XML::Streamer lStreamer(lOutStream);
lStreamer.openTag("Population");
for(int j = 0; j < lNbIndividual; ++j){
(*lBuffer)[j+lNbIndividualTotal]->write(lStreamer, false);
}
lStreamer.closeTag();
lStreams[i] = lOutStream.str();
lRequests[i] = new MPICommunication::Request;
mComm->sendNonBlocking(lStreams[i], lRequests[i], "Individuals", "Child", i);
lNbIndividualTotal += lNbIndividual;
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"distribute", "Beagle::HPC::DistributeDemeToEvaluatorsOp",
std::string("Evolver send fractionnal Deme to his ")+uint2ordinal(i+1)+ " evaluator"
);
}
mComm->waitAll(lRequests);
Beagle_StackTraceEndM("DistributeDemeToEvaluatorsOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Check if the maximum fitness value is reached.
* \param inDeme Actual deme of the evolution.
* \param ioContext Actual evolution context.
* \return True if the ending criterion is reached, false if not.
*/
bool TermMaxFitnessOp::terminate(const Deme& inDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
for(unsigned int i=0; i<inDeme.size(); ++i) {
FitnessSimple::Handle lFitness =
castHandleT<FitnessSimple>(inDeme[i]->getFitness());
if(lFitness->isValid() && lFitness->getValue() >= mMaxFitness->getWrappedValue()) {
Beagle_LogInfoM(
ioContext.getSystem().getLogger(),
std::string("Maximum fitness value (") +
dbl2str(mMaxFitness->getWrappedValue()) +
std::string(") termination criterion reached by the ") +
uint2ordinal(i+1) + std::string(" individual (") +
dbl2str(lFitness->getValue()) + std::string(")")
);
ioContext.setTerminationSuccessful();
return true;
}
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Maximum fitness value (") +
dbl2str(mMaxFitness->getWrappedValue()) +
std::string(") termination criterion not reached ")
);
return false;
Beagle_StackTraceEndM();
}
/*!
* \brief Receive a deme content from an evolver node.
* \param ioDeme Deme to update by the receive deme.
* \param ioContext Current context of the evolution.
*/
void HPC::RecvDemeFromEvolverOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::string lNbrProcessed;
std::string lDemeString;
mComm->receive(lNbrProcessed, "NbrProcessed", "Child", ioContext.getDemeIndex());
mComm->receive(lDemeString, "Deme", "Child", ioContext.getDemeIndex());
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"receive", "Beagle::HPC::RecvDemeFromEvolverOp",
std::string("Supervisor receive deme from his ")+
uint2ordinal(ioContext.getDemeIndex()+1)+std::string(" evolver")
);
prepareStats(ioDeme,ioContext);
std::istringstream lInStream(lDemeString);
PACC::XML::Document lDocument(lInStream);
ioDeme.readPopulation(lDocument.getFirstRoot(), ioContext);
updateStats(str2uint(lNbrProcessed), ioContext);
updateHallOfFameWithDeme(ioDeme,ioContext);
Beagle_StackTraceEndM("void HPC::RecvDemeFromEvolverOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Send the individuals that were modified during the current generation.
* \param ioDeme Current deme to execute the operator.
* \param ioContext Current context to execute the operator.
* \todo Check if this operator can be used with migration operator.
* This operator can only be used in a context where the size of the
* population remains constant for all generations.
*/
void HPC::SendProcessedToSupervisorOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
ProcessingBuffer::Handle lBuffer = castHandleT<ProcessingBuffer>(ioDeme.getMember("ProcessingBuffer"));
Beagle_NonNullPointerAssertM(lBuffer);
std::ostringstream lOutStream;
PACC::XML::Streamer lStreamer(lOutStream);
lStreamer.openTag("Population");
for(unsigned int i = 0; i < lBuffer->size(); ++i)
(*lBuffer)[i]->write(lStreamer,false);
lStreamer.closeTag();
mComm->send(uint2str(ioContext.getProcessedDeme()), "NbrProcessed", "Parent");
mComm->send(lBuffer->getIndex().serialize(), "ProcessedIndex", "Parent");
mComm->send(lOutStream.str(), "Processed", "Parent");
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"send", "Beagle::HPC::SendProcessedToSupervisorOp",
std::string("Evolver send deme to his supervisor")
);
Beagle_StackTraceEndM("void HPC::SendProcessedToSupervisorOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Receive the fitness of an individuals group from evaluator node.
* \param ioDeme Deme to update by the receive fitness.
* \param ioContext Current context of the evolution.
*/
void HPC::RecvFitnessFromEvaluatorOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
ProcessingBuffer::Handle lBuffer = castHandleT<ProcessingBuffer>(ioDeme.getMember("ProcessingBuffer"));
Beagle_NonNullPointerAssertM(lBuffer);
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
prepareStats(ioDeme,ioContext);
unsigned int lNbEvaluators = mComm->getNbrOfRelation("Child");
unsigned int lNbIndividualInt = lBuffer->size() / lNbEvaluators;
unsigned int lNbIndividualFrac = lBuffer->size() % lNbEvaluators;
unsigned int lNbIndividualTotal = 0;
for(int i = 0; i < lNbEvaluators; ++i ){
int lNbIndividual = lNbIndividualInt;
if(i < lNbIndividualFrac)
++lNbIndividual;
std::string lFitnessString;
mComm->receive(lFitnessString, "Fitness", "Child", i);
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"receive", "Beagle::HPC::RecvFitnessFromEvaluatorOp",
std::string("Evolver receive fitness from his ")+uint2ordinal(i+1)+
std::string(" evaluator") + std::string(" of ") + uint2str(lNbEvaluators)
);
std::istringstream lInStream(lFitnessString);
PACC::XML::Document lDocument(lInStream);
const Factory& lFactory = ioContext.getSystem().getFactory();
Fitness::Alloc::Handle lFitnessAlloc =
castHandleT<Fitness::Alloc>(lFactory.getConceptAllocator("Fitness"));
for(PACC::XML::ConstIterator lIter = lDocument.getFirstRoot()->getFirstChild(); lIter; ++lIter){
ioContext.setIndividualIndex(lNbIndividualTotal);
ioContext.setIndividualHandle(ioDeme[lNbIndividualTotal]);
if((*lBuffer)[lNbIndividualTotal]->getFitness() == 0)
(*lBuffer)[lNbIndividualTotal]->setFitness( castHandleT<Fitness>(lFitnessAlloc->allocate()) );
(*lBuffer)[lNbIndividualTotal]->getFitness()->read(lIter);
++lNbIndividualTotal;
updateStats(1,ioContext);
}
}
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"receive", "Beagle::HPC::RecvFitnessFromEvaluatorOp",
std::string("Evolver receive all its fitness.")
);
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
Beagle_StackTraceEndM("void RecvFitnessFromEvaluatorOp::operate(Deme& ioDeme, Context& ioContext)");
}
bool TreeSTag::findMatchingTopology(Deme& ioDeme, Context& ioContext, TreeSTag::Handle& outTree) {
for(unsigned int i=0; i<ioDeme.size(); ++i) {
TreeSTag::Handle lTree = castHandleT<TreeSTag>((*(ioDeme)[i])[0]);
if(lTree != this) {
if(this->compareTopology(*lTree)) {
outTree = lTree;
return true;
}
}
}
return false;
}
/*!
* \brief Read individuals from a given file to seed the evolution.
* \param inFileName File name to read seeds individual from.
* \param ioDeme Deme to initialize with seeds.
* \param ioContext Evolutionary context.
* \return Number of seeds read.
*
* Seeds file format is quite simple: XML file with "Beagle" root tag, and then a
* "Seeds" tag with in it the individuals representation to read. Here is a
* seeds file example with one individual in it.
* \verbatim
<?xml version="1.0" encoding="ISO-8859-1"?>
<Beagle>
<Seeds>
<Individual>
<Genotype type="bitstring">11111</Genotype>
</Individual>
</Seeds>
</Beagle>
\endverbatim
* If there is less individuals in the seed file than the population size, the
* remaining individuals are initialized as usual. If there is more individuals
* than needed, the last individuals of the seeds file are ignored. If more than one
* deme is used in the evolution, each deme will be seeded with the same seeds file.
*
*/
unsigned int InitializationOp::readSeeds(std::string inFileName,
Deme& ioDeme,
Context& ioContext)
{
Beagle_StackTraceBeginM();
#ifdef BEAGLE_HAVE_LIBZ
igzstream lIFStream(inFileName.c_str());
#else // BEAGLE_HAVE_LIBZ
std::ifstream lIFStream(inFileName.c_str());
#endif // BEAGLE_HAVE_LIBZ
PACC::XML::Document lParser;
try {
lParser.parse(lIFStream, inFileName);
} catch(IOException& inExcept) {
std::ostringstream lOSS;
lOSS << "The seeds file is invalid: " << inExcept.what();
throw Beagle_IOExceptionMessageM(lOSS.str());
}
unsigned int lReadIndividuals=0;
unsigned int lOldIndivIndex = ioContext.getIndividualIndex();
Individual::Handle lOldIndivHandle = ioContext.getIndividualHandle();
for(PACC::XML::ConstIterator lNode=lParser.getFirstRoot(); lNode; ++lNode) {
if((lNode->getType()==PACC::XML::eData) && (lNode->getValue()=="Beagle")) {
for(PACC::XML::ConstIterator lChild=lNode->getFirstChild(); lChild; ++lChild) {
if((lChild->getType()==PACC::XML::eData) && (lChild->getValue()=="Seeds")) {
for(PACC::XML::ConstIterator lChild2=lChild->getFirstChild(); lChild2; ++lChild2) {
if((lChild2->getType()==PACC::XML::eData) && (lChild2->getValue()=="Individual")) {
if(lReadIndividuals >= ioDeme.size()) break;
Beagle_NonNullPointerAssertM(ioDeme[lReadIndividuals]);
ioContext.setIndividualIndex(lReadIndividuals);
ioContext.setIndividualHandle(ioDeme[lReadIndividuals]);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Reading the ")+uint2ordinal(lReadIndividuals+1)+
std::string(" individual from seeds file")
);
ioDeme[lReadIndividuals]->readWithContext(lChild2, ioContext);
Beagle_LogDebugM(ioContext.getSystem().getLogger(), *ioDeme[lReadIndividuals]);
++lReadIndividuals;
}
}
}
}
}
}
ioContext.setIndividualHandle(lOldIndivHandle);
ioContext.setIndividualIndex(lOldIndivIndex);
return lReadIndividuals;
Beagle_StackTraceEndM();
}
void Beagle::MPI::EvaluationOp::evolverOperate(Deme& ioDeme, Context& ioContext) {
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
std::string("Evaluating the individuals fitness of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
if(ioDeme.size() == 0)
return;
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
ioContext.setProcessedDeme(0);
if((ioContext.getGeneration()!=0) && (ioDeme.getStats()->existItem("total-processed"))) {
ioContext.setTotalProcessedDeme((unsigned int)ioDeme.getStats()->getItem("total-processed"));
}
else ioContext.setTotalProcessedDeme(0);
ioDeme.getStats()->setInvalid();
if(ioContext.getDemeIndex()==0) {
Stats& lVivaStats = *ioContext.getVivarium().getStats();
ioContext.setProcessedVivarium(0);
if((ioContext.getGeneration()!=0) && (lVivaStats.existItem("total-processed"))) {
ioContext.setTotalProcessedVivarium((unsigned int)lVivaStats.getItem("total-processed"));
}
else ioContext.setTotalProcessedVivarium(0);
lVivaStats.setInvalid();
}
distributeDemeEvaluation(ioDeme, ioContext);
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
if(mDemeHOFSize->getWrappedValue() > 0) {
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
"Updating the deme's hall-of-fame"
);
ioDeme.getHallOfFame().updateWithDeme(mDemeHOFSize->getWrappedValue(), ioDeme, ioContext);
ioDeme.getHallOfFame().log(Logger::eVerbose, ioContext);
}
if(mVivaHOFSize->getWrappedValue() > 0) {
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"evaluation", "Beagle::MPIEvaluationOp",
"Updating the vivarium's hall-of-fame"
);
ioContext.getVivarium().getHallOfFame().updateWithDeme(mVivaHOFSize->getWrappedValue(),
ioDeme, ioContext);
ioContext.getVivarium().getHallOfFame().log(Logger::eVerbose, ioContext);
}
}
/*!
* \brief Apply the operation on a deme in the given context.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
*/
void GenerationalOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(getRootNode());
Beagle_NonNullPointerAssertM(mElitismKeepSize);
Beagle_ValidateParameterM(mElitismKeepSize->getWrappedValue() <= ioDeme.size(),
"ec.elite.keepsize",
"The elistism keepsize must be less than the deme size!");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Processing using generational replacement strategy the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
Beagle_LogTraceM(ioContext.getSystem().getLogger(), (*this));
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
Individual::Bag lOffsprings;
const Factory& lFactory = ioContext.getSystem().getFactory();
if(mElitismKeepSize->getWrappedValue() > 0) {
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
for(unsigned int i=0; i<mElitismKeepSize->getWrappedValue(); ++i) {
std::string lIndividualType = ioDeme[0]->getType();
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getAllocator(lIndividualType));
Individual::Handle lEliteIndiv = castHandleT<Individual>(lIndividualAlloc->allocate());
lEliteIndiv->copy(*ioDeme[0], ioContext.getSystem());
lOffsprings.push_back(lEliteIndiv);
if(lHistory != NULL) {
HistoryID::Handle lHID = castHandleT<HistoryID>(ioDeme[0]->getMember("HistoryID"));
std::vector<HistoryID> lParent;
if(lHID != NULL) lParent.push_back(*lHID);
lHistory->allocateNewID(*lEliteIndiv);
lHistory->trace(ioContext, lParent, lEliteIndiv, getName(), "elitism");
}
std::pop_heap(ioDeme.begin(), (ioDeme.end()-i), IsLessPointerPredicate());
}
}
for(unsigned int i=mElitismKeepSize->getWrappedValue(); i<ioDeme.size(); ++i) {
unsigned int lIndexBreeder = lRoulette.select(ioContext.getSystem().getRandomizer());
BreederNode::Handle lSelectedBreeder=getRootNode();
for(unsigned int j=0; j<lIndexBreeder; ++j)
lSelectedBreeder=lSelectedBreeder->getNextSibling();
Beagle_NonNullPointerAssertM(lSelectedBreeder);
Beagle_NonNullPointerAssertM(lSelectedBreeder->getBreederOp());
Individual::Handle lBredIndiv =
lSelectedBreeder->getBreederOp()->breed(ioDeme, lSelectedBreeder->getFirstChild(), ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
lOffsprings.push_back(lBredIndiv);
}
for(unsigned int j=0; j<lOffsprings.size(); ++j) ioDeme[j] = lOffsprings[j];
Beagle_StackTraceEndM();
}
/*!
* \brief Distribute demes to evolver nodes.
* \param ioDeme Current deme to execute the operator.
* \param ioContext Current context to execute the operator.
*/
void HPC::SendDemeToEvolverOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
unsigned int lChild = ioContext.getDemeIndex();
std::ostringstream lOutStream;
PACC::XML::Streamer lStreamer(lOutStream);
ioDeme.write(lStreamer, false);
mComm->send(lOutStream.str(), "Deme", "Child", lChild);
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
std::string("Send ") + uint2ordinal(ioContext.getDemeIndex()) + " deme to his " + uint2ordinal(lChild) + " evolver"
);
Beagle_StackTraceEndM();
}
/*!
* \brief Receive a deme content from supervisor node.
* \param ioDeme Deme to update by the receive deme.
* \param ioContext Current context of the evolution.
*/
void HPC::RecvDemeFromSupervisorOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::string lDemeString;
mComm->receive(lDemeString, "Deme", "Parent");
std::istringstream lInStream(lDemeString);
PACC::XML::Document lDocument(lInStream);
ioDeme.readWithContext(lDocument.getFirstRoot(), ioContext);
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"receive", "Beagle::HPC::RecvDemeFromSupervisorOp",
std::string("Receive ") + uint2ordinal( ioContext.getDemeIndex() ) + std::string(" deme from supervisor") //remplacer (1) par l'index du deme
);
Beagle_StackTraceEndM();
}
/*!
* \brief Construct the SendLogToParentOp operator.
* \param ioDeme Current deme to execute the operator.
* \param ioContext Current context to execute the operator.
*/
void HPC::SendDemeToSupervisorOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::ostringstream lOutStream;
PACC::XML::Streamer lStreamer(lOutStream);
ioDeme.writePopulation(lStreamer,false);
mComm->send(uint2str(ioContext.getProcessedDeme()), "NbrProcessed", "Parent");
mComm->send(lOutStream.str(), "Deme", "Parent");
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"send", "Beagle::HPC::SendDemeToSupervisorOp",
std::string("Evolver send deme to his supervisor")
);
Beagle_StackTraceEndM("void HPC::SendDemeToSupervisorOp::operate(Deme&, Context&)");
}
/*!
* \brief Invalidates the fitness of every individual in ioDeme.
* \param ioDeme The deme to operate on.
* \param ioContext Evolutionary context.
*/
void InvalidateFitnessOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Invalidating the fitness of every individual in the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
for(unsigned int i=0; i<ioDeme.size(); i++) {
if(ioDeme[i]->getFitness() != NULL) {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Invalidating the fitness of the " << uint2ordinal(i+1) <<
" individual of the " << uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
ioDeme[i]->getFitness()->setInvalid();
}
}
Beagle_StackTraceEndM();
}
/*!
* \brief Receive a group of individuals to evaluate from the parent evolver node.
* \param ioDeme Current deme to evaluate the individus group.
* \param ioContext Current context of the evolution.
*/
void HPC::RecvIndividualsFromEvolverOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
std::string lPopulationString;
mComm->receive(lPopulationString, "Individuals", "Parent");
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"receive", "Beagle::HPC::RecvIndividualsFromEvolverOp",
std::string("Evaluator receive individuals from his parent evolver")
);
std::istringstream lInStream(lPopulationString);
PACC::XML::Document lDocument(lInStream);
ioDeme.readPopulation(lDocument.getFirstRoot(),ioContext);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply NSGA2 multiobjective selection operator as a standard operator.
* \param ioDeme Deme on which selection operator is applied.
* \param ioContext Evolutionary context.
*/
void EMO::NSGA2Op::applyAsStandardOperator(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
// Fast non-dominated sorting, followed by insertion of the first Pareto fronts.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Applying fast non-dominated sorting on the whole population"
);
NSGA2Op::Fronts lParetoFronts;
const unsigned int lDesiredPopSize = (*mPopSize)[ioContext.getDemeIndex()];
Individual::Bag lSortedPop(ioDeme);
sortFastND(lParetoFronts, lDesiredPopSize, lSortedPop, ioContext);
unsigned int lIndexDeme=0;
for(unsigned int j=0; j<(lParetoFronts.size()-1); ++j) {
for(unsigned int k=0; k<lParetoFronts[j].size(); ++k) {
ioDeme[lIndexDeme++] = lSortedPop[lParetoFronts[j][k]];
}
}
// Insertion of the last Pareto front, using crowding distance
Individual::Bag lLastFrontIndiv;
for(unsigned int l=0; l<lParetoFronts.back().size(); ++l) {
lLastFrontIndiv.push_back(lSortedPop[lParetoFronts.back()[l]]);
}
NSGA2Op::Distances lDistances;
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Computing crowding distance on the " << uint2ordinal(lParetoFronts.size()) <<
" Pareto front, which is made of " << uint2ordinal(lParetoFronts.back().size()) << " individuals"
);
evalCrowdingDistance(lDistances, lLastFrontIndiv);
for(unsigned int m=0; lIndexDeme<lDesiredPopSize; ++m) {
ioDeme[lIndexDeme++] = lLastFrontIndiv[lDistances[m].second];
}
ioDeme.resize(lDesiredPopSize);
Beagle_StackTraceEndM();
}
void StatsCalcFitnessNMSEOp::calculateStatsDeme(Stats &outStats, Deme &ioDeme, Context &ioContext) const {
Beagle_StackTraceBeginM();
outStats.clear();
outStats.clearItems();
int outputs = mConfig->getOutputs().size();
outStats.addItem("processed", ioContext.getProcessedDeme());
outStats.addItem("total-processed", ioContext.getTotalProcessedDeme());
if(ioDeme.size() == 0) {
outStats.setGenerationValues(Beagle::string("deme")+uint2str(ioContext.getDemeIndex()+1),
ioContext.getGeneration(), 0, true);
outStats.resize(3+outputs*2);
outStats[0].mId = "NMSE";
outStats[0].mAvg = 0.0;
outStats[0].mStd = 0.0;
outStats[0].mMax = 0.0;
outStats[0].mMin = 0.0;
outStats[1].mId = "treedepth";
outStats[1].mAvg = 0.0;
outStats[1].mStd = 0.0;
outStats[1].mMax = 0.0;
outStats[1].mMin = 0.0;
outStats[2].mId = "treesize";
outStats[2].mAvg = 0.0;
outStats[2].mStd = 0.0;
outStats[2].mMax = 0.0;
outStats[2].mMin = 0.0;
for(int i=0; i<outputs; ++i) {
int nr = 3 + i*2;
outStats[nr].mId = "y" + int2str(i) + "-NMSE";
outStats[nr].mAvg = 0.0;
outStats[nr].mStd = 0.0;
outStats[nr].mMax = 0.0;
outStats[nr].mMin = 0.0;
++nr;
outStats[nr].mId = "y" + int2str(i) + "-MSE";
outStats[nr].mAvg = 0.0;
outStats[nr].mStd = 0.0;
outStats[nr].mMax = 0.0;
outStats[nr].mMin = 0.0;
}
return;
}
const GP::Deme& gpDeme = castObjectT<const GP::Deme&>(ioDeme);
const FitnessNMSE::Handle firstIndivFitness = castHandleT<FitnessNMSE>(ioDeme[0]->getFitness());
if(ioDeme.size() == 1) {
outStats.setGenerationValues(Beagle::string("deme")+uint2str(ioContext.getDemeIndex()+1),
ioContext.getGeneration(), 1, true);
outStats.resize(3+outputs*2);
outStats[0].mId = "NMSE";
outStats[0].mAvg = firstIndivFitness->getNMSE();
outStats[0].mStd = 0.0;
outStats[0].mMax = firstIndivFitness->getNMSE();
outStats[0].mMin = firstIndivFitness->getNMSE();
outStats[1].mId = "treedepth";
outStats[1].mAvg = gpDeme[0]->getMaxTreeDepth();
outStats[1].mStd = 0.0;
outStats[1].mMax = outStats[1].mAvg;
outStats[1].mMin = outStats[1].mAvg;
outStats[2].mId = "treesize";
outStats[2].mAvg = gpDeme[0]->getTotalNodes();
outStats[2].mStd = 0.0;
outStats[2].mMax = outStats[2].mAvg;
outStats[2].mMin = outStats[2].mAvg;
for(int i=0; i<outputs; ++i) {
int nr = 3 + i*2;
double nmse = (*firstIndivFitness)[i].nmse;
double mse = (*firstIndivFitness)[i].mse;
outStats[nr].mId = "y" + int2str(i) + "-NMSE";
outStats[nr].mAvg = nmse;
outStats[nr].mStd = 0.0;
outStats[nr].mMax = nmse;
outStats[nr].mMin = nmse;
++nr;
outStats[nr].mId = "y" + int2str(i) + "-MSE";
outStats[nr].mAvg = mse;
outStats[nr].mStd = 0.0;
outStats[nr].mMax = mse;
outStats[nr].mMin = mse;
}
return;
}
double sum = firstIndivFitness->getNMSE();
double pow2sum = pow2Of<double>(sum);
double max = sum;
double min = sum;
std::vector<double> sumNMSE(outputs, 0);
std::vector<double> pow2sumNMSE(outputs, 0);
std::vector<double> maxNMSE(outputs, 0);
std::vector<double> minNMSE(outputs, 0);
std::vector<double> sumMSE(outputs, 0);
std::vector<double> pow2sumMSE(outputs, 0);
std::vector<double> maxMSE(outputs, 0);
std::vector<double> minMSE(outputs, 0);
for(int i=0; i<outputs; ++i) {
double nmse = (*firstIndivFitness)[i].nmse;
double mse = (*firstIndivFitness)[i].mse;
sumNMSE[i] = nmse;
pow2sumNMSE[i] = pow2Of<double>(nmse);
maxNMSE[i] = nmse;
minNMSE[i] = nmse;
sumMSE[i] = mse;
pow2sumMSE[i] = pow2Of<double>(mse);
maxMSE[i] = mse;
minMSE[i] = mse;
}
unsigned int lMaxDepth = gpDeme[0]->getMaxTreeDepth();
unsigned int lMinDepth = lMaxDepth;
double lSumDepth = (double)lMaxDepth;
double lPow2SumDepth = pow2Of<double>(lSumDepth);
unsigned int lMaxSize = gpDeme[0]->getTotalNodes();
unsigned int lMinSize = lMaxSize;
double lSumSize = (double)lMaxSize;
double lPow2SumSize = pow2Of<double>(lSumSize);
unsigned indivs = 0;
for(unsigned int i=1; i<ioDeme.size(); i++) {
const FitnessNMSE::Handle indivFitness = castHandleT<FitnessNMSE>(ioDeme[i]->getFitness());
double tNmse = indivFitness->getNMSE();
//cout << endl << i << "\t" << tNmse << "\t" << indivFitness->size();
if(tNmse != tNmse || tNmse == numeric_limits<double>::infinity()) {
continue;
}
++indivs;
sum += tNmse;
pow2sum += pow2Of<double>(tNmse);
max = maxOf<double>(max, tNmse);
min = minOf<double>(min, tNmse);
for(int j=0; j<outputs; ++j) {
double nmse = (*indivFitness)[j].nmse;
double mse = (*indivFitness)[j].mse;
sumNMSE[j] += nmse;
pow2sumNMSE[j] += pow2Of<double>(nmse);
maxNMSE[j] = maxOf<double>(maxNMSE[j], nmse);
minNMSE[j] = minOf<double>(minNMSE[j], nmse);
sumMSE[j] += mse;
pow2sumMSE[j] += pow2Of<double>(mse);
maxMSE[j] = maxOf<double>(maxMSE[j], mse);
minMSE[j] = minOf<double>(minMSE[j], mse);
}
unsigned int lTmpDepth = gpDeme[i]->getMaxTreeDepth();
lSumDepth += (double)lTmpDepth;
lPow2SumDepth += pow2Of<double>((double)lTmpDepth);
lMaxDepth = maxOf(lMaxDepth, lTmpDepth);
lMinDepth = minOf(lMinDepth, lTmpDepth);
unsigned int lTmpSize = gpDeme[i]->getTotalNodes();
lSumSize += (double)lTmpSize;
lPow2SumSize += pow2Of<double>((double)lTmpSize);
lMaxSize = maxOf(lMaxSize, lTmpSize);
lMinSize = minOf(lMinSize, lTmpSize);
}
float lDepthStdError =
(float)(lPow2SumDepth - (pow2Of<double>(lSumDepth) / indivs)) / (indivs - 1);
lDepthStdError = sqrt(lDepthStdError);
float lSizeStdError =
(float)(lPow2SumSize - (pow2Of<double>(lSumSize) / indivs)) / (indivs - 1);
lSizeStdError = sqrt(lSizeStdError);
outStats.setGenerationValues(Beagle::string("deme")+uint2str(ioContext.getDemeIndex()+1),
ioContext.getGeneration(),
ioDeme.size(),
true);
outStats.resize(3+outputs*2);
outStats[0].mId = "NMSE";
outStats[0].mAvg = sum / indivs;
outStats[0].mStd = sqrt((pow2sum - (pow2Of<double>(sum)/indivs)) / (indivs-1));
outStats[0].mMax = max;
outStats[0].mMin = min;
outStats[1].mId = "treedepth";
outStats[1].mAvg = (float)(lSumDepth / indivs);
outStats[1].mStd = lDepthStdError;
outStats[1].mMax = (float)lMaxDepth;
outStats[1].mMin = (float)lMinDepth;
outStats[2].mId = "treesize";
outStats[2].mAvg = (float)(lSumSize / indivs);
outStats[2].mStd = lSizeStdError;
outStats[2].mMax = (float)lMaxSize;
outStats[2].mMin = (float)lMinSize;
for(int j=0; j<outputs; ++j) {
int nr = 3 + j*2;
outStats[nr].mId = "y" + int2str(j) + "-NMSE";
outStats[nr].mAvg = sumNMSE[j] / indivs;
outStats[nr].mStd = sqrt((pow2sumNMSE[j] - (pow2Of<double>(sumNMSE[j])/indivs)) / (indivs-1));
outStats[nr].mMax = maxNMSE[j];
outStats[nr].mMin = minNMSE[j];
++nr;
outStats[nr].mId = "y" + int2str(j) + "-MSE";
outStats[nr].mAvg = sumMSE[j] / indivs;
outStats[nr].mStd = sqrt((pow2sumMSE[j] - (pow2Of<double>(sumMSE[j])/indivs)) / (indivs-1));
outStats[nr].mMax = maxMSE[j];
outStats[nr].mMin = minMSE[j];
}
Beagle_StackTraceEndM("void SinsGP::StatsCalcFitnessNMSEOp::calculateStatsDeme(Beagle::Stats& outStats, Beagle::Deme& ioDeme, Beagle::Context& ioContext) const");
}
/*!
* \brief Apply the evaluation process on the invalid individuals of the deme.
* \param ioDeme Deme to process.
* \param ioContext Context of the evolution.
*/
void EvaluationMultipleOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Evaluating the fitness of the individuals in the " <<
uint2ordinal(ioContext.getDemeIndex()+1) << " deme"
);
Beagle_AssertM( ioDeme.size()!=0 );
// Prepare stats
prepareStats(ioDeme,ioContext);
// Generate a vector of indicies into the population
std::vector<unsigned int> lEvalVector;
for(unsigned int i=0; i<ioDeme.size(); i++) {
if((ioDeme[i]->getFitness() == NULL) ||
(ioDeme[i]->getFitness()->isValid() == false)) {
lEvalVector.push_back(i);
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Added " << uint2ordinal(i+1) << " individual for evaluation."
);
}
}
std::random_shuffle(lEvalVector.begin(), lEvalVector.end(),
ioContext.getSystem().getRandomizer());
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"There are " << lEvalVector.size() << " individuals to be evaluated."
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
while ( !lEvalVector.empty() ) {
// Put individuals and context into bags.
Individual::Bag lIndividuals;
Context::Bag lContexts;
lIndividuals.resize( mIndisPerGroup );
lContexts.resize( mIndisPerGroup );
unsigned int lIndiCounter =0;
for (unsigned int i=0; i<mIndisPerGroup; i++) {
// Set individual
lIndividuals[i] = ioDeme[lEvalVector.back()];
lIndiCounter++;
// Set context
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext = castHandleT<Context>(lContextAlloc->clone(ioContext));
lContext->setIndividualIndex( lEvalVector.back() );
lContext->setIndividualHandle( ioDeme[lEvalVector.back()] );
lContexts[i] = lContext;
// Remove this index from the evaluation vector
lEvalVector.pop_back();
if(lEvalVector.empty()) {
lIndividuals.resize( lIndiCounter );
lContexts.resize( lIndiCounter );
break;
}
}
// Evaluate individuals
std::ostringstream lOSS;
lOSS << "Evaluating the fitness of the ";
for(unsigned int i=0; i<lIndiCounter; i++) {
// Add to message
if (i==lIndiCounter-1) lOSS << " and ";
lOSS << uint2ordinal(lContexts[i]->getIndividualIndex()+1);
if (i<lIndiCounter-2) lOSS << ", ";
}
lOSS << " individuals";
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
lOSS.str()
);
Fitness::Bag::Handle lFitnessBag = evaluateIndividuals(lIndividuals, lContexts);
// Assign fitnesses
for (unsigned int i=0; i<lIndiCounter; i++) {
Beagle_LogDebugM(
ioContext.getSystem().getLogger(),
"Considering fitness of the " << uint2ordinal(lContexts[i]->getIndividualIndex()+1) << " individual"
);
Beagle_AssertM( i < lFitnessBag->size() );
Fitness::Handle lFitness = lFitnessBag->at(i);
Beagle_NonNullPointerAssertM( lFitness );
lIndividuals[i]->setFitness( lFitness );
lIndividuals[i]->getFitness()->setValid();
if(lHistory != NULL) {
lHistory->allocateID(*lIndividuals[i]);
lHistory->trace(ioContext, std::vector<HistoryID>(), lIndividuals[i], getName(), "evaluation");
}
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
*lIndividuals[i]->getFitness()
);
}
// Update stats
updateStats(lIndividuals.size(),ioContext);
}
updateHallOfFameWithDeme(ioDeme,ioContext);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the decimation operation on the deme.
* \param ioDeme Current deme of individuals to decimate.
* \param ioContext Context of the evolution.
*/
void DecimateOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM((mDecimationRatio->getWrappedValue()<=1.0),
mDecimationRatioName,
"The decimation ratio must be less than or equal to 1.0.");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("Applying decimation operation on the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
// Calculate the number of individuals to keep from the deme
unsigned int lMu = 0;
if(mDecimationRatio->getWrappedValue() == -1.0) {
Beagle_AssertM(ioContext.getDemeIndex() < mPopSize->size());
lMu = (*mPopSize)[ioContext.getDemeIndex()];
} else {
lMu = (unsigned int)std::ceil(mDecimationRatio->getWrappedValue()*float(ioDeme.size()));
Beagle_AssertM(ioContext.getDemeIndex() < mPopSize->size());
int lDiffSize = (*mPopSize)[ioContext.getDemeIndex()] - lMu;
if((lDiffSize >= -1) && (lDiffSize <= 1)) lMu = (*mPopSize)[ioContext.getDemeIndex()];
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("Keeping ")+uint2str(lMu)+" of the "+uint2str(ioDeme.size())+
" individuals from the "+uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
// Check that the number of individuals to keep (mu) isn't greater than the deme size
if(lMu > ioDeme.size()) {
std::ostringstream lOSS;
lOSS << "Warning: the actual population size (" << ioDeme.size();
lOSS << ") is less than the desired decimation size (" << lMu;
lOSS << "). Decimation is thus not applied.";
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
lOSS.str()
);
return;
}
// Copy the individuals to be kept into the deme
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
Individual::Bag lSurvivors;
for(unsigned int i=0; i<lMu; ++i) {
lSurvivors.push_back(ioDeme.front());
std::pop_heap(ioDeme.begin(), (ioDeme.end()-i), IsLessPointerPredicate());
}
ioDeme.clear();
ioDeme.insert(ioDeme.begin(), lSurvivors.begin(), lSurvivors.end());
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"decimation", "Beagle::DecimateOp",
std::string("There are now ")+uint2str(ioDeme.size())+" individuals in the "+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_StackTraceEndM("void DecimateOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Calculate the statistics of the current deme/generation.
* \param ioDeme Actual deme of the evolution.
* \param ioContext Context of the evolution.
*/
void StatsCalculateOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"stats", "Beagle::StatsCalculateOp",
string("Calculating stats for the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
if(ioContext.getGeneration() != mGenerationCalculated) {
mGenerationCalculated = ioContext.getGeneration();
mNbDemesCalculated = 0;
}
if(ioDeme.getStats() == NULL) {
const Factory& lFactory = ioContext.getSystem().getFactory();
Stats::Alloc::Handle lStatsAlloc =
castHandleT<Stats::Alloc>(lFactory.getConceptAllocator("Stats"));
Stats::Handle lStats = castHandleT<Stats>(lStatsAlloc->allocate());
ioDeme.addMember(lStats);
}
if(ioDeme.getStats()->isValid() == false) {
calculateStatsDeme(*ioDeme.getStats(), ioDeme, ioContext);
ioDeme.getStats()->setValid();
}
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eStats,
"stats",
"Beagle::StatsCalculateOp",
*ioDeme.getStats()
);
if(++mNbDemesCalculated == mPopSize->size()) {
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"stats", "Beagle::StatsCalculateOp",
"Calculating stats for the vivarium"
);
if(ioContext.getVivarium().getStats() == NULL) {
const Factory& lFactory = ioContext.getSystem().getFactory();
Stats::Alloc::Handle lStatsAlloc =
castHandleT<Stats::Alloc>(lFactory.getConceptAllocator("Stats"));
Stats::Handle lStats = castHandleT<Stats>(lStatsAlloc->allocate());
ioContext.getVivarium().addMember(lStats);
}
calculateStatsVivarium(*ioContext.getVivarium().getStats(),
ioContext.getVivarium(),
ioContext);
ioContext.getVivarium().getStats()->setValid();
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eStats,
"stats", "Beagle::StatsCalculateOp",
*ioContext.getVivarium().getStats()
);
}
Beagle_StackTraceEndM("void StatsCalculateOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Update covariance matrix, cumulation path and other CMA values.
* \param ioDeme Deme to use to update CMA values.
* \param ioContext Evolutionary context.
* \param inN Dimensionality of the problem.
* \param inMuEff Effective mu.
* \param inSelectionWeights Selection weights.
* \param ioCMAValues Reference to CMA values.
*
* This routine is mostly inspired from matlab routine cmaes.m and the document
* "The CMA Evolution Strategy: A Tutorial" (October 15, 2004), both
* from Nikolaus Hansen.
* See http://www.bionik.tu-berlin.de/user/niko/cmaes_inmatlab.html
*/
void CMA::MuWCommaLambdaCMAFltVecOp::updateValues(Deme& ioDeme,
Context& ioContext,
unsigned int inN,
double inMuEff,
const Vector& inSelectionWeights,
CMA::CMAValues& ioCMAValues) const
{
Beagle_StackTraceBeginM();
// Log messages
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"Updating covariance matrix, sigma, and cumulation paths of CMA-ES."
);
// Compute some constants
const double lCC = 4.0 / (double(inN) + 4.0);
const double lCS = (inMuEff+2.0) / (double(inN)+inMuEff+3.0);
const double lMuCov = inMuEff;
double lCCov = ((2.0*inMuEff)-1.0) / (((double(inN)+2.0)*(double(inN)+2.0)) + inMuEff);
lCCov = ((1.0/lMuCov) * (2.0/((double(inN)+1.414)*(double(inN)+1.414)))) +
((1.0-(1.0/lMuCov)) * minOf(1.0,lCCov));
double lDamps = std::sqrt((inMuEff-1.0) / (double(inN)+1.0)) - 1.0;
lDamps = 1.0 + (2.0*maxOf(0.0,lDamps)) + lCS;
const double lChiN = std::sqrt(double(inN)) *
(1.0 - (0.25/double(inN)) + (1.0/(21.0*double(inN)*double(inN))));
// Compute new xmean
Vector lXmean_new(inN, 0.0);
for(unsigned int i=0; i<ioDeme.size(); ++i) {
FltVec::FloatVector::Handle lVecI = castHandleT<FltVec::FloatVector>((*ioDeme[i])[0]);
for(unsigned int j=0; j<inN; ++j) lXmean_new[j] += (inSelectionWeights[i] * (*lVecI)[j]);
}
// Compute zmean
Vector lZmean(inN,0.0);
const double lSigma=ioCMAValues.mSigma.getWrappedValue();
for(unsigned int i=0; i<inN; ++i) {
lZmean[i] = (lXmean_new[i] - ioCMAValues.mXmean[i]) / lSigma;
}
Matrix lBt;
ioCMAValues.mB.transpose(lBt);
lZmean = lBt * lZmean;
for(unsigned int i=0; i<inN; ++i) lZmean[i] /= ioCMAValues.mD[i];
// Update cumulation paths
Matrix lBD(inN,inN,0.0);
for(unsigned int i=0; i<inN; ++i) {
for(unsigned int j=0; j<inN; ++j) lBD(j,i) = ioCMAValues.mB(j,i) * ioCMAValues.mD[i];
}
Vector lBZm;
ioCMAValues.mB.multiply((Matrix&)lBZm, lZmean);
lBZm *= std::sqrt(lCS * (2.0-lCS) * inMuEff);
ioCMAValues.mPS *= (1.0-lCS);
ioCMAValues.mPS += lBZm;
double lPSnorm = 0.0;
for(unsigned int i=0; i<ioCMAValues.mPS.size(); ++i) lPSnorm += (ioCMAValues.mPS[i] * ioCMAValues.mPS[i]);
lPSnorm = std::sqrt(lPSnorm);
const double lHLeft =
lPSnorm / std::sqrt(1.0-std::pow(1.0-lCS, 2.0*double(ioContext.getGeneration())));
const double lHRight = (1.5+(1.0/(double(inN)-0.5))) * lChiN;
const bool lHSig = (lHLeft<lHRight);
ioCMAValues.mPC *= (1.0-lCC);
if(lHSig) {
// Vector lBDZm;
// lBD.multiply((Matrix&)lBDZm, lZmean);
// lBDZm *= std::sqrt(lCC * (2.0-lCC) * inMuEff);
// ioCMAValues.mPC += lBDZm;
Vector lXdiff = lXmean_new - ioCMAValues.mXmean;
lXdiff *= (std::sqrt(lCC * (2.0-lCC) * inMuEff) / lSigma);
ioCMAValues.mPC += lXdiff;
} else {
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"CMA-ES p_c cumulation path update stalled"
);
}
// Adapt covariance matrix C
Matrix lC, lBDt;
lBD.transpose(lBDt);
lBD.multiply(lC, lBDt);
double lAttnC = (1.0-lCCov); // Attenuation factor
if(lHSig == false) lAttnC += (lCCov * lCC * (2.0-lCC) / lMuCov);
Matrix lR1Upd; // Rank one update
ioCMAValues.mPC.transpose(lR1Upd);
lR1Upd = ioCMAValues.mPC * lR1Upd;
lR1Upd *= (lCCov / lMuCov);
Matrix lRMuUpd(inN,inN,0.0); // Rank Mu update
for(unsigned int i=0; i<ioDeme.size(); ++i) {
FltVec::FloatVector::Handle lVecI = castHandleT<FltVec::FloatVector>((*ioDeme[i])[0]);
Vector lX_I(lVecI->size());
for(unsigned int j=0; j<lVecI->size(); ++j) lX_I[j] = (*lVecI)[j];
lX_I -= ioCMAValues.mXmean;
Matrix lX_It;
lX_I.transpose(lX_It);
lX_It *= inSelectionWeights[i];
lRMuUpd += (lX_I * lX_It);
}
lRMuUpd *= (lCCov * (1.0 - (1.0/lMuCov)) / (lSigma * lSigma));
lC *= lAttnC; // Attenuate old matrix
lC += lR1Upd; // Add rank one update
lC += lRMuUpd; // Add rank mu update
// Adapt step size sigma
ioCMAValues.mSigma.getWrappedValue() *= std::exp((lCS/lDamps) * ((lPSnorm/lChiN)-1.0));
// Update B and D from C
for(unsigned int i=1; i<inN; ++i) {
for(unsigned int j=0; j<i; ++j) lC(i,j) = lC(j,i); // Enforce symetry
}
lC.computeEigens(ioCMAValues.mD, ioCMAValues.mB); // Principal component analysis
// Adjust D as standard deviation
for(unsigned int i=0; i<inN; ++i) {
ioCMAValues.mD[i] = std::sqrt(ioCMAValues.mD[i]);
}
// Log updated parameters.
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("CMA-ES updated B matrix (principal components): ")+ioCMAValues.mB.serialize()
);
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("CMA-ES updated D vector (standard deviations): ")+ioCMAValues.mD.serialize()
);
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("CMA-ES updated sigma: ")+ioCMAValues.mSigma.serialize()
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("CMA-ES updated p_c vector (covariance cumulation path): ")+ioCMAValues.mPC.serialize()
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("CMA-ES updated p_s vector (sigma cumulation path): ")+ioCMAValues.mPS.serialize()
);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply NSGA2 multiobjective selection operator as a replacement strategy.
* \param ioDeme Deme on which selection operator is applied.
* \param ioContext Evolutionary context.
*/
void EMO::NSGA2Op::applyAsReplacementStrategy(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Processing using NSGA2 replacement strategy the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogTraceM(ioContext.getSystem().getLogger(), (*this));
// Generate a new generation of individuals, merged with the actual one.
const unsigned int lLambda =
(unsigned int)std::ceil(mLMRatio->getWrappedValue()*float(ioDeme.size()));
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Generating " << lLambda << " offsprings using breeder tree"
);
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
Individual::Bag lOffsprings(ioDeme);
for(unsigned int i=0; i<lLambda; ++i) {
unsigned int lIndexBreeder = lRoulette.select(ioContext.getSystem().getRandomizer());
BreederNode::Handle lSelectedBreeder=getRootNode();
for(unsigned int j=0; j<lIndexBreeder; ++j)
lSelectedBreeder=lSelectedBreeder->getNextSibling();
Beagle_NonNullPointerAssertM(lSelectedBreeder);
Beagle_NonNullPointerAssertM(lSelectedBreeder->getBreederOp());
Individual::Handle lBredIndiv =
lSelectedBreeder->getBreederOp()->breed(ioDeme, lSelectedBreeder->getFirstChild(), ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
lOffsprings.push_back(lBredIndiv);
}
// Fast non-dominated sorting, followed by insertion of the first Pareto fronts.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Applying fast non-dominated sorting on the union of parents and offsprings individual"
);
NSGA2Op::Fronts lParetoFronts;
sortFastND(lParetoFronts, ioDeme.size(), lOffsprings, ioContext);
unsigned int lIndexDeme=0;
for(unsigned int j=0; j<(lParetoFronts.size()-1); ++j) {
for(unsigned int k=0; k<lParetoFronts[j].size(); ++k) {
ioDeme[lIndexDeme++] = lOffsprings[lParetoFronts[j][k]];
}
}
// Insertion of the last Pareto front, using crowding distance
Individual::Bag lLastFrontIndiv;
for(unsigned int l=0; l<lParetoFronts.back().size(); ++l) {
lLastFrontIndiv.push_back(lOffsprings[lParetoFronts.back()[l]]);
}
NSGA2Op::Distances lDistances;
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
"Computing crowding distance on the " << uint2ordinal(lParetoFronts.size()) <<
" Pareto front, which is made of " << lParetoFronts.back().size() << " individuals"
);
evalCrowdingDistance(lDistances, lLastFrontIndiv);
for(unsigned int m=0; lIndexDeme<ioDeme.size(); ++m) {
ioDeme[lIndexDeme++] = lLastFrontIndiv[lDistances[m].second];
}
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the initialization operation on the deme.
* \param ioDeme Current deme of individuals to initialize.
* \param ioContext Context of the evolution.
*/
void InitializationOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
#ifndef BEAGLE_NDEBUG
if(ioContext.getVivariumHandle()!=NULL) {
Beagle_AssertM(mPopSize->size() == ioContext.getVivarium().size());
}
#endif // BEAGLE_NDEBUG
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Initializing the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
if(!ioDeme.empty()) {
Beagle_LogBasicM(
ioContext.getSystem().getLogger(),
std::string("Warning! Applying '")+getName()+"' will overwrite the "+
uint2str(ioDeme.size())+" individual(s) currently in the deme with newly initialized "+
"individuals. If this is not what you desire consider using OversizeOp instead."
);
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Resizing the deme from ")+
uint2str(ioDeme.size())+" to "+
uint2str((*mPopSize)[ioContext.getDemeIndex()])+" individuals"
);
const Factory& lFactory = ioContext.getSystem().getFactory();
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
ioDeme.clear();
const unsigned int lDemeSize = (*mPopSize)[ioContext.getDemeIndex()];
for(unsigned int i=0; i<lDemeSize; ++i) {
ioDeme.push_back(lIndividualAlloc->allocate());
}
unsigned int lSeededIndividuals = 0;
if(mSeedsFile->getWrappedValue().empty() == false) {
Beagle_LogInfoM(
ioContext.getSystem().getLogger(),
std::string("Reading seeds file '")+mSeedsFile->getWrappedValue()+
std::string("' to initialize the ")+uint2ordinal(ioContext.getDemeIndex()+1)+
std::string(" deme")
);
lSeededIndividuals = readSeeds(mSeedsFile->getWrappedValue(), ioDeme, ioContext);
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
uint2str(lSeededIndividuals)+std::string(" individuals read to seed the deme")
);
}
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
for(unsigned int i=lSeededIndividuals; i<ioDeme.size(); ++i) {
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Initializing the ")+uint2ordinal(i+1)+" individual"
);
ioContext.setIndividualHandle(ioDeme[i]);
ioContext.setIndividualIndex(i);
initIndividual(*ioDeme[i], ioContext);
if(ioDeme[i]->getFitness() != NULL) {
ioDeme[i]->getFitness()->setInvalid();
}
if(lHistory != NULL) {
lHistory->incrementHistoryVar(*ioDeme[i]);
lHistory->trace(ioContext, std::vector<HistoryID>(), ioDeme[i], getName(), "initialization");
}
}
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the oversize replacement strategy operation on a deme.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
*/
void OversizeOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_NonNullPointerAssertM(getRootNode());
Beagle_ValidateParameterM
(mOversizeRatio->getWrappedValue() >= 1.0
|| mOversizeRatio->getWrappedValue() == -1.0,
mOversizeRatioName,
"The oversize ratio must be greater than or equal to 1.0, or equal to -1.0.");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("Using oversize replacement strategy to process the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogObjectM(
ioContext.getSystem().getLogger(),
Logger::eTrace,
"replacement-strategy", "Beagle::OversizeOp",
(*this)
);
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
// Calculate the increase in size (lambda)
float lRatio = mOversizeRatio->getWrappedValue();
unsigned int lLambda;
if (lRatio == -1.0) {
// Using special ratio of -1.0 ensures deme grows to size specified in 'ec.pop.size'
if (!ioContext.getSystem().getRegister().isRegistered("ec.pop.size")) {
throw Beagle_RunTimeExceptionM(getName()+" requires register variable 'ec.pop.size'");
}
UIntArray::Handle lPopSize = castHandleT<UIntArray>
(ioContext.getSystem().getRegister().getEntry("ec.pop.size"));
unsigned int lSpecifiedDemeSize = (*lPopSize)[ioContext.getDemeIndex()];
unsigned int lCurrentDemeSize = ioDeme.size();
if (lSpecifiedDemeSize < lCurrentDemeSize) {
throw Beagle_RunTimeExceptionM
(std::string("For the ")+uint2ordinal(ioContext.getDemeIndex()+1)+
" deme, the size specified in 'ec.pop.size' ("+uint2str(lSpecifiedDemeSize)+
") is less than the current deme size ("+uint2str(lCurrentDemeSize)+
"). "+getName()+" can only increase the size of the deme. Consider using DecimateOp "+
"if you wish to decrease the size of the deme");
}
lLambda = lSpecifiedDemeSize - lCurrentDemeSize;
} else {
// Using ratio to scale the deme's population
lLambda = (unsigned int)ceil((lRatio-1.0)*float(ioDeme.size()));
}
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("Population will be increased in size by ")+uint2str(lLambda)+" individuals"
);
// Create the new individuals.
Individual::Bag lOffsprings;
for(unsigned int i=0; i<lLambda; ++i) {
unsigned int lIndexBreeder = lRoulette.select(ioContext.getSystem().getRandomizer());
BreederNode::Handle lSelectedBreeder=getRootNode();
for(unsigned int j=0; j<lIndexBreeder; ++j)
lSelectedBreeder=lSelectedBreeder->getNextSibling();
Beagle_NonNullPointerAssertM(lSelectedBreeder);
Beagle_NonNullPointerAssertM(lSelectedBreeder->getBreederOp());
Individual::Handle lBredIndiv =
lSelectedBreeder->getBreederOp()->breed(ioDeme, lSelectedBreeder->getFirstChild(), ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
lOffsprings.push_back(lBredIndiv);
}
// Add the new individuals into the deme.
ioDeme.insert(ioDeme.end(), lOffsprings.begin(), lOffsprings.end());
Beagle_LogDetailedM(
ioContext.getSystem().getLogger(),
"replacement-strategy", "Beagle::OversizeOp",
string("There are now ")+uint2str(ioDeme.size())+" individuals in the "+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_StackTraceEndM("void OversizeOp::operate(Deme& ioDeme, Context& ioContext)");
}
/*!
* \brief Apply the CMA-ES (Mu_W+Lambda) replacement strategy operation on a deme.
* \param ioDeme Reference to the deme on which the operation takes place.
* \param ioContext Evolutionary context of the operation.
* \throw Beagle::ValidationException If a parameter is missing or have a bad value.
* \throw Beagle::AssertException If an invalid condition appears.
*/
void CMA::MuWCommaLambdaCMAFltVecOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
// Get real popsize and size of float vectors from register.
UIntArray::Handle lPopSize;
if(ioContext.getSystem().getRegister().isRegistered("ec.pop.size")) {
lPopSize = castHandleT<UIntArray>(ioContext.getSystem().getRegister()["ec.pop.size"]);
} else {
std::ostringstream lOSS;
lOSS << "Population size parameter 'ec.pop.size' is not found in register!";
throw ValidationException(lOSS.str());
}
const unsigned int lDemeSize = (*lPopSize)[ioContext.getDemeIndex()];
UInt::Handle lFloatVectorSize;
if(ioContext.getSystem().getRegister().isRegistered("ga.init.vectorsize")) {
lFloatVectorSize = castHandleT<UInt>(ioContext.getSystem().getRegister()["ga.init.vectorsize"]);
} else {
std::ostringstream lOSS;
lOSS << "GA::MuWCommaLambdaCMAFltVecOp must be used in fixed-lenght float vector ";
lOSS << "individuals. Parameter 'ga.init.vectorsize' is not in register, ";
lOSS << "while it is needed to set initial size of the different CMA-ES matrices ";
lOSS << "and vectors.";
throw ValidationException(lOSS.str());
}
const unsigned int lN=lFloatVectorSize->getWrappedValue();
// Get the appropriate CMA values from the CMA holder component.
CMA::CMAValues& lValues = getCMAValues(ioContext.getDemeIndex(),lN,ioContext);
// Compute weights and effective mu
Vector lWeight;
double lMuEff = 0.0;
lMuEff = generateSelectionWeights(lDemeSize, lWeight);
if(ioDeme.size() == 1) lMuEff = 1.;
// If the replacement strategy possess a breeder tree
if(getRootNode()!=NULL) {
// Generate new children.
const unsigned int lLambda =
(unsigned int)std::ceil(mLMRatio->getWrappedValue()*double(lDemeSize));
generateChildren(ioDeme, ioContext, lLambda, lN, lValues, lWeight);
// Check if all individuals have known fitness.
for(unsigned int i=0; i<ioDeme.size(); ++i) {
// If there is one invalid fitness, we should exit.
// Evaluation will be taken elsewhere (we hope), and actual operator will be recalled.
if((ioDeme[i]->getFitness()==NULL) || (ioDeme[i]->getFitness()->isValid()==false)) return;
}
}
// Keep mu best children
Beagle_AssertM(ioDeme.size() > lDemeSize);
std::sort(ioDeme.begin(), ioDeme.end(), IsMorePointerPredicate());
ioDeme.resize(lDemeSize);
// Update CMA-ES values.
updateValues(ioDeme, ioContext, lN, lMuEff, lWeight, lValues);
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the recombination operation on the deme.
* \param ioDeme Current deme of individuals to recombine.
* \param ioContext Context of the evolution.
*/
void RecombinationOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mRecombProba->getWrappedValue()>=0.0, mRecombProbaName, "<0");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals with probability ")+
dbl2str(mRecombProba->getWrappedValue())
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Bag lRecombinedIndiv(ioDeme.size());
for(unsigned int i=0; i<lRecombinedIndiv.size(); ++i) {
if(ioContext.getSystem().getRandomizer().rollUniform() <= mRecombProba->getWrappedValue()) {
Individual::Bag::Handle lParents = new Individual::Bag;
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? ioDeme.size() :
minOf<unsigned int>(ioDeme.size(), mNumberRecomb->getWrappedValue());
if(lNbGenerated == ioDeme.size()) (*lParents) = ioDeme;
else {
std::vector<unsigned int> lIndices(ioDeme.size());
for(unsigned int j=0; j<lIndices.size(); ++j) lIndices[j] = j;
std::random_shuffle(lIndices.begin(), lIndices.end(),
ioContext.getSystem().getRandomizer());
for(unsigned int j=0; j<lNbGenerated; ++j) {
lParents->push_back(ioDeme[lIndices[j]]);
}
}
lRecombinedIndiv[i] = recombine(*lParents, ioContext);
if(lRecombinedIndiv[i]->getFitness() != NULL) {
lRecombinedIndiv[i]->getFitness()->setInvalid();
}
// Log and update history.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("The ")+uint2ordinal(i+1)+
std::string(" individual as been replaced by recombination")
);
if(lHistory != NULL) {
std::vector<HistoryID> lParentNames;
for(unsigned int j=0; j<lParents->size(); ++j) {
HistoryID::Handle lHID = castHandleT<HistoryID>(lParents->at(j)->getMember("HistoryID"));
if(lHID != NULL) lParentNames.push_back(*lHID);
}
lHistory->incrementHistoryVar(*lRecombinedIndiv[i]);
lHistory->trace(ioContext, lParentNames, lRecombinedIndiv[i], getName(), "recombination");
}
}
}
for(unsigned int i=0; i<ioDeme.size(); ++i) {
if(lRecombinedIndiv[i] != NULL) ioDeme[i] = lRecombinedIndiv[i];
}
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the crossover operation on the deme.
* \param ioDeme Current deme of individuals to mate.
* \param ioContext Context of the evolution.
*/
void CrossoverOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mMatingProba->getWrappedValue()>=0.0, mMatingProbaName, "<0");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Mating individuals of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Mating individuals with probability ")+
dbl2str(mMatingProba->getWrappedValue())
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Handle lOldIndividualHandle = ioContext.getIndividualHandle();
unsigned int lOldIndividualIndex = ioContext.getIndividualIndex();
std::vector<unsigned int> lMateVector;
for(unsigned int i=0; i<ioDeme.size(); i++) {
if(ioContext.getSystem().getRandomizer().rollUniform() <= mMatingProba->getWrappedValue()) {
lMateVector.push_back(i);
}
}
std::random_shuffle(lMateVector.begin(), lMateVector.end(),
ioContext.getSystem().getRandomizer());
if((lMateVector.size() % 2) != 0) lMateVector.pop_back();
int j = 0;
int lSize = lMateVector.size();
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
static OpenMP::Handle lOpenMP = castHandleT<OpenMP>(ioContext.getSystem().getComponent("OpenMP"));
const Factory& lFactory = ioContext.getSystem().getFactory();
const std::string& lContextName = lFactory.getConceptTypeName("Context");
Context::Alloc::Handle lContextAlloc = castHandleT<Context::Alloc>(lFactory.getAllocator(lContextName));
Context::Bag lContexts(lOpenMP->getMaxNumThreads());
Context::Bag lContexts2(lOpenMP->getMaxNumThreads());
for(unsigned int i = 0; i < lOpenMP->getMaxNumThreads(); ++i) {
lContexts[i] = castHandleT<Context>(lContextAlloc->clone(ioContext));
lContexts2[i] = castHandleT<Context>(lContextAlloc->clone(ioContext));
}
#if defined(BEAGLE_USE_OMP_NR)
#pragma omp parallel for shared(lSize, lMateVector, lHistory, lContexts, lContexts2) private(j) schedule(dynamic)
#elif defined(BEAGLE_USE_OMP_R)
const int lChunkSize = std::max((int)(lSize / lOpenMP->getMaxNumThreads()), 1);
#pragma omp parallel for shared(lSize, lMateVector, lHistory, lContexts, lContexts2) private(j) schedule(static, lChunkSize)
#endif
#else
Context::Alloc::Handle lContextAlloc =
castHandleT<Context::Alloc>(ioContext.getSystem().getFactory().getConceptAllocator("Context"));
Context::Handle lContext2 = castHandleT<Context>(lContextAlloc->clone(ioContext));
#endif
for(j=0; j<lSize; j+=2) {
unsigned int lFirstMate = lMateVector[j];
unsigned int lSecondMate = lMateVector[j+1];
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
lContexts[lOpenMP->getThreadNum()]->setIndividualIndex(lFirstMate);
lContexts[lOpenMP->getThreadNum()]->setIndividualHandle(ioDeme[lFirstMate]);
lContexts2[lOpenMP->getThreadNum()]->setIndividualIndex(lSecondMate);
lContexts2[lOpenMP->getThreadNum()]->setIndividualHandle(ioDeme[lSecondMate]);
#else
ioContext.setIndividualIndex(lFirstMate);
ioContext.setIndividualHandle(ioDeme[lFirstMate]);
lContext2->setIndividualIndex(lSecondMate);
lContext2->setIndividualHandle(ioDeme[lSecondMate]);
#endif
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Mating the ")+uint2ordinal(lFirstMate+1)+
std::string(" individual with the ")+uint2ordinal(lSecondMate+1)+" individual"
);
std::vector<HistoryID> lParents;
if(lHistory != NULL) {
#pragma omp critical (Beagle_History)
{
HistoryID::Handle lHID1 = castHandleT<HistoryID>(ioDeme[lFirstMate]->getMember("HistoryID"));
if(lHID1 != NULL) lParents.push_back(*lHID1);
HistoryID::Handle lHID2 = castHandleT<HistoryID>(ioDeme[lSecondMate]->getMember("HistoryID"));
if(lHID2 != NULL) lParents.push_back(*lHID2);
}
}
#if defined(BEAGLE_USE_OMP_NR) || defined(BEAGLE_USE_OMP_R)
bool lMated = mate(*ioDeme[lFirstMate], *(lContexts[lOpenMP->getThreadNum()]), *ioDeme[lSecondMate], *(lContexts2[lOpenMP->getThreadNum()]));
#else
bool lMated = mate(*ioDeme[lFirstMate], ioContext, *ioDeme[lSecondMate], *lContext2);
#endif
if(lMated) {
if(ioDeme[lFirstMate]->getFitness() != NULL) {
ioDeme[lFirstMate]->getFitness()->setInvalid();
}
if(ioDeme[lSecondMate]->getFitness() != NULL) {
ioDeme[lSecondMate]->getFitness()->setInvalid();
}
if(lHistory != NULL) {
#pragma omp critical (Beagle_History)
{
lHistory->incrementHistoryVar(*ioDeme[lFirstMate]);
#if defined(BEAGLE_USE_OMP_R) || defined(BEAGLE_USE_OMP_NR)
lHistory->trace(*lContexts[lOpenMP->getThreadNum()], lParents, ioDeme[lFirstMate], getName(), "crossover");
#else
lHistory->trace(ioContext, lParents, ioDeme[lFirstMate], getName(), "crossover");
#endif
lHistory->incrementHistoryVar(*ioDeme[lSecondMate]);
#if defined(BEAGLE_USE_OMP_R) || defined(BEAGLE_USE_OMP_NR)
lHistory->trace(*lContexts[lOpenMP->getThreadNum()], lParents, ioDeme[lSecondMate], getName(), "crossover");
#else
lHistory->trace(ioContext, lParents, ioDeme[lSecondMate], getName(), "crossover");
#endif
}
}
}
}
ioContext.setIndividualIndex(lOldIndividualIndex);
ioContext.setIndividualHandle(lOldIndividualHandle);
Beagle_StackTraceEndM();
}
/*!
* \brief Generate children from the breeder tree.
* \param ioDeme Deme to generate children from.
* \param ioContext Evolutionary context.
* \param lNbChildren Number of children to generate.
* \param inN Dimensionality of the problem.
* \param ioCMAValues CMA values to use to generate new individual.
* \param inSelectionWeights Selection weights used to generate children.
*/
void CMA::MuWCommaLambdaCMAFltVecOp::generateChildren(Deme& ioDeme,
Context& ioContext,
unsigned int inNbChildren,
unsigned int inN,
CMAValues& ioCMAValues,
const Vector& inSelectionWeights) const
{
Beagle_StackTraceBeginM();
// Check parameters and log some information
Beagle_NonNullPointerAssertM(mElitismKeepSize);
Beagle_ValidateParameterM(mLMRatio->getWrappedValue() >= 1.0,
mLMRatioName,
"The LM ratio must be higher or equal to 1.0.");
Beagle_ValidateParameterM(mElitismKeepSize->getWrappedValue() <= ioDeme.size(),
"ec.elite.keepsize",
"The elistism keepsize must be less than the deme size!");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Using CMA-ES (mu_w,lambda) replacement strategy to process the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogTraceM(ioContext.getSystem().getLogger(), (*this));
const Factory& lFactory = ioContext.getSystem().getFactory();
// Create weighted mean individual.
std::sort(ioDeme.begin(), ioDeme.end(), IsMorePointerPredicate());
Individual::Alloc::Handle lIndividualAlloc =
castHandleT<Individual::Alloc>(lFactory.getConceptAllocator("Individual"));
Individual::Handle lMeanInd = castHandleT<Individual>(lIndividualAlloc->allocate());
Genotype::Alloc::Handle lGenotypeAlloc =
castHandleT<Genotype::Alloc>(lFactory.getConceptAllocator("Genotype"));
FltVec::FloatVector::Handle lMeanFloatVec =
castHandleT<FltVec::FloatVector>(lGenotypeAlloc->allocate());
lMeanFloatVec->resize(inN);
lMeanInd->push_back(lMeanFloatVec);
for(unsigned int i=0; i<inN; ++i) (*lMeanFloatVec)[i] = 0.0;
if(ioDeme.size()==1) {
Beagle_AssertM(ioDeme[0]->size() == 1);
FltVec::FloatVector::Handle lInd = castHandleT<FltVec::FloatVector>((*ioDeme[0])[0]);
(*lMeanFloatVec) = *lInd;
} else {
for(unsigned int i=0; i<ioDeme.size(); ++i) {
Beagle_AssertM(ioDeme[i]->size()==1);
FltVec::FloatVector::Handle lVecI = castHandleT<FltVec::FloatVector>((*ioDeme[i])[0]);
Beagle_AssertM(lVecI->size()==inN);
for(unsigned int j=0; j<inN; ++j) (*lMeanFloatVec)[j] += (inSelectionWeights[i] * (*lVecI)[j]);
}
}
ioCMAValues.mXmean.resize(inN);
for(unsigned int i=0; i<inN; ++i) ioCMAValues.mXmean[i] = (*lMeanFloatVec)[i];
// Generate lambda children with breeder tree, first build breeder roulette
RouletteT<unsigned int> lRoulette;
buildRoulette(lRoulette, ioContext);
// Keep best individuals if elitism is used
const unsigned int lElitismKS=mElitismKeepSize->getWrappedValue();
if(lElitismKS > 0) {
Individual::Bag lBestInd;
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
std::make_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
for(unsigned int i=0; i<lElitismKS; ++i) {
if(lHistory != NULL) {
HistoryID::Handle lHID = castHandleT<HistoryID>(ioDeme[0]->getMember("HistoryID"));
std::vector<HistoryID> lParent;
if(lHID != NULL) lParent.push_back(*lHID);
lHistory->allocateNewID(*ioDeme[0]);
lHistory->trace(ioContext, lParent, ioDeme[0], getName(), "elitism");
}
lBestInd.push_back(ioDeme[0]);
std::pop_heap(ioDeme.begin(), ioDeme.end(), IsLessPointerPredicate());
ioDeme.pop_back();
}
ioDeme.clear();
ioDeme.insert(ioDeme.end(), lBestInd.begin(), lBestInd.end());
} else ioDeme.clear();
// Generate the children
Individual::Bag lBagWithMeanInd;
lBagWithMeanInd.push_back(lMeanInd);
for(unsigned int i=0; i<inNbChildren; ++i) {
unsigned int lIndexBreeder = lRoulette.select(ioContext.getSystem().getRandomizer());
BreederNode::Handle lSelectedBreeder=getRootNode();
for(unsigned int j=0; j<lIndexBreeder; ++j)
lSelectedBreeder=lSelectedBreeder->getNextSibling();
Beagle_NonNullPointerAssertM(lSelectedBreeder);
Beagle_NonNullPointerAssertM(lSelectedBreeder->getBreederOp());
Individual::Handle lBredIndiv =
lSelectedBreeder->getBreederOp()->breed(lBagWithMeanInd,
lSelectedBreeder->getFirstChild(),
ioContext);
Beagle_NonNullPointerAssertM(lBredIndiv);
ioDeme.push_back(lBredIndiv);
}
Beagle_StackTraceEndM();
}