EvolutionaryAlgorithm.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Vishwesh Venkatraman <vishwesh.venkatraman@ntnu.no>
 * 
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program 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 Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.ga;
 
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.Future;
import java.util.concurrent.RejectedExecutionHandler;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import java.util.logging.Level;
import java.util.logging.Logger;
 
import org.apache.commons.lang3.time.StopWatch;
import org.openscience.cdk.io.iterator.IteratingSMILESReader;
 
import denoptim.exception.DENOPTIMException;
import denoptim.exception.ExceptionUtils;
import denoptim.fitness.FitnessParameters;
import denoptim.ga.EAUtils.CandidateSource;
import denoptim.graph.Candidate;
import denoptim.io.IteratingAtomContainerReader;
import denoptim.logging.CounterID;
import denoptim.logging.Monitor;
import denoptim.programs.RunTimeParameters.ParametersType;
import denoptim.programs.denovo.GAParameters;
import denoptim.programs.fragmenter.FragmenterParameters;
import denoptim.task.FitnessTask;
import denoptim.task.Task;
import denoptim.task.TasksBatchManager;
import denoptim.utils.SizeControlledSet;
 
public class EvolutionaryAlgorithm
{
    final ExternalCmdsListener cmdListener;
    
    private SizeControlledSet scs;
    
    private boolean stopped = false;
    
    private Set<String> candidatesToRemove = new HashSet<String>();
    
    private List<String> candidatesToAdd = new ArrayList<String>();
 
    private boolean isAsync = true;
    
    private Map<FitnessTask,Future<Object>> futures;
    
    private List<FitnessTask> submitted;
    
    private ThreadPoolExecutor tpe;
    
    private TasksBatchManager tbm;
 
    private Throwable ex;
    
    private GAParameters settings;
 
    private Logger logger = null;
    
    private final String NL = System.getProperty("line.separator");
 
//------------------------------------------------------------------------------
 
    public EvolutionaryAlgorithm(GAParameters settings, 
            ExternalCmdsListener cmdListener)
    {
        this.settings = settings;
        this.logger = settings.getLogger();
        this.cmdListener = cmdListener;
        
        // There is currently nothing to initialize for the synchronous scheme
        if (settings.getParallelizationScheme() == 1)
        {
            isAsync = false;
            tbm = new TasksBatchManager();
            
        } else {
            isAsync = true;
            futures = new HashMap<FitnessTask,Future<Object>>();
            submitted = new ArrayList<>();
            
            tpe = new ThreadPoolExecutor(settings.getNumberOfCPU(),
                    settings.getNumberOfCPU(), 0L,
                    TimeUnit.MILLISECONDS,
                    new ArrayBlockingQueue<Runnable>(1));
    
            Runtime.getRuntime().addShutdownHook(new Thread()
            {
                @Override
                public void run()
                {
                    tpe.shutdown(); // Disable new tasks from being submitted
                    try
                    {
                        // Wait a while for existing tasks to terminate
                        if (!tpe.awaitTermination(30, TimeUnit.SECONDS))
                        {
                            tpe.shutdownNow(); //Cancel running tasks
                        }
                        if (!tpe.awaitTermination(60, TimeUnit.SECONDS))
                        {
                            // pool didn't terminate after the second try
                        }
                    }
                    catch (InterruptedException ie)
                    {
                        cleanupAsync();
                        // (Re-)Cancel if current thread also interrupted
                        tpe.shutdownNow();
                        // Preserve interrupt status
                        Thread.currentThread().interrupt();
                    }
                }
            });
    
            // by default the ThreadPoolExecutor will throw an exception
            tpe.setRejectedExecutionHandler(new RejectedExecutionHandler()
            {
                @Override
                public void rejectedExecution(Runnable r, 
                        ThreadPoolExecutor executor)
                {
                    try
                    {
                        // this will block if the queue is full
                        executor.getQueue().put(r);
                    }
                    catch (InterruptedException ex)
                    {
                        //nothing, really
                    }
                }
            });
        }
        
        scs = new SizeControlledSet(
                settings.maxUIDMemory, settings.uidMemoryOnDisk, 
                settings.getUIDFileOut());
    }
 
//------------------------------------------------------------------------------
    
    public void run() throws DENOPTIMException
    {
        cmdListener.setReferenceToRunningEAlgorithm(this);
        
        StopWatch watch = new StopWatch();
        watch.start();
        if (isAsync)
        {
            tpe.prestartAllCoreThreads();
        }
        Monitor mnt = new Monitor();
        mnt.printHeader(settings.getMonitorFile());
        
        // Create initial population of candidates
        EAUtils.createFolderForGeneration(0, settings);
        Population population;
        try
        {
            population = EAUtils.importInitialPopulation(scs, settings);
        } catch (Exception e)
        {
            throw new DENOPTIMException("Unable to import initial population.", 
                    e);
        }
        initializePopulation(population);
        
        boolean writeCandsOnDisk = ((FitnessParameters) settings.getParameters(
                ParametersType.FIT_PARAMS)).writeCandidatesOnDisk();
        EAUtils.outputPopulationDetails(population, 
                EAUtils.getPathNameToGenerationDetailsFile(0, settings), 
                settings, writeCandsOnDisk);
        
        // Ensure that there is some variability in fitness values
        double sdev = EAUtils.getPopulationSD(population);
        if (sdev < settings.getMinFitnessSD())
        {
            String msg = "Fitness values have negligible standard deviation "
                    + "(STDDEV=" + String.format("%.6f", sdev) + "). "
                    + "Abbandoning evolutionary algorithm.";
            logger.log(Level.SEVERE, msg);
            population.trim(0);
            return;
        }
 
        // Start evolution cycles, i.e., generations
        int numStag = 0, genId = 1;
        while (genId <= settings.getNumberOfGenerations())
        {
            logger.log(Level.INFO,"Starting Generation {0}"
                    + NL, genId);
 
            String txt = "No change";
            try
            {
                if (!evolvePopulation(population, genId))
                {
                    numStag++;
                }
                else
                {
                    numStag = 0;
                    txt = "New members introduced";
                }
            } catch (DENOPTIMException e)
            {
                logger.log(Level.SEVERE, "Exception while running evolutionary"
                        + "algorithm. Details: " + NL 
                        + ExceptionUtils.getStackTraceAsString(e));
                throw e;
            }
            
            logger.log(Level.INFO,txt + " in Generation {0}" 
                    + NL, genId);
            EAUtils.outputPopulationDetails(population, 
                    EAUtils.getPathNameToGenerationDetailsFile(genId, settings),
                    settings, writeCandsOnDisk);
            
            if (stopped)
            {
                logger.log(Level.SEVERE, 
                        "EA stopped while working on generation {0}. " + NL
                        + "Reporting data for incomplete generation {0}."
                        + NL,genId);
                break;
            } else {
                logger.log(Level.INFO,
                        "Generation {0}" + " completed" + NL
                        + "----------------------------------------"
                        + "----------------------------------------" 
                        + NL, genId);
            }
 
            if (numStag >= settings.getNumberOfConvergenceGenerations())
            {
                logger.log(Level.WARNING, 
                        "No change in population over {0} iterations. "
                        + "Stopping EA." + NL, numStag);
                break;
            }
 
            genId++;
        }
        
        if (isAsync)
        {
            tpe.shutdown();
            try
            {
                // wait a bit for pending tasks to finish
                while (!tpe.awaitTermination(5, TimeUnit.SECONDS))
                {
                    // do nothing
                }
            }
            catch (InterruptedException ex)
            {
                //Do nothing
            }
            tpe.shutdown();
        }
 
        // Sort the population and trim it to desired size
        Collections.sort(population, Collections.reverseOrder());
        if (settings.getReplacementStrategy() == 1)
        {
            population.trim(settings.getPopulationSize());
        }
 
        // And write final results
        EAUtils.outputFinalResults(population, settings);
        
        // Termination
        population.trim(0);
        watch.stop();
        logger.log(Level.INFO, "Overall time: {0}." + NL,
                watch.toString());
        
        if (stopped)
        {
            logger.info("DENOPTIM EA run stopped." + NL);
        } else {
            logger.info("DENOPTIM EA run completed." + NL);
        }
    }
 
//------------------------------------------------------------------------------
 
    private void initializePopulation(Population population) 
            throws DENOPTIMException
    {
        // Deal with existing initial population members
        synchronized (population)
        {
            if (stopped)
            {
                return;
            }
            
            // Keep only the best candidates if there are too many.
            Collections.sort(population, Collections.reverseOrder());
            if (settings.getReplacementStrategy() == 1 && 
                    population.size() > settings.getPopulationSize())
            {
                population.trim(settings.getPopulationSize());
            }
        }
        // NB: pop size cannot be > because it has been just trimmed
        if (population.size() == settings.getPopulationSize())
        {
            return;
        }
        
        Monitor mnt = new Monitor("MonitorGen",0,settings.getMonitorFile(),
                settings.getMonitorDumpStep(), settings.dumpMonitor(),
                settings.getLogger());
        
        // Screen molecules (these can be very many!)
        if (settings.getInitMolsToFragmentFile()!=null)
        {
            IteratingAtomContainerReader iterMolsToFragment = null;
            try
            {
                iterMolsToFragment = new IteratingAtomContainerReader(new File(
                        settings.getInitMolsToFragmentFile()));
                if (iterMolsToFragment.getIteratorType().equals(
                        IteratingSMILESReader.class))
                {
                    FragmenterParameters frgParams = new FragmenterParameters();
                    if (settings.containsParameters(ParametersType.FRG_PARAMS))
                    {
                        frgParams = (FragmenterParameters) 
                                settings.getParameters(
                                        ParametersType.FRG_PARAMS);
                    }
                    frgParams.setWorkingIn3D(false);
                }
            } catch (Exception e1)
            {
                throw new DENOPTIMException("Could not set reader on file ''"
                        + settings.getInitMolsToFragmentFile() + ".", ex);
            }
            
            // This is very similar to the standard population initialization 
            // async loop, but it allows to screen many more candidates because
            // it keeps only best N, where N is the size of the population.
            // Yet, there is plenty of repeated code, which is sub-optimal.
            int i=0;
            List<Task> batchOfSyncParallelTasks = new ArrayList<>();
            try 
            {
                while (iterMolsToFragment.hasNext()) 
                {
                    i++;
                    
                    if (stopped)
                    {
                        break;
                    }
                    
                    if (checkForException())
                    {
                        stopRun();
                        throw new DENOPTIMException("Errors found during sub "
                                + "tasks execution.", ex);
                    }
                    
                    Candidate candidate = 
                            EAUtils.buildCandidateByFragmentingMolecule(
                                iterMolsToFragment.next(), mnt, settings, i);
 
                    // NB: here we request to keep only the best candidates
                    // so that the tmp population does not become too large
                    // before being trimmed.
                    i = processInitialPopCandidate(candidate, population, mnt, 
                            batchOfSyncParallelTasks, i, true, true);
                }
                // We still need to submit the possibly partially-filled last batch
                if (batchOfSyncParallelTasks.size()>0)
                    submitSyncParallelBatch(batchOfSyncParallelTasks);
            } catch (DENOPTIMException dex)
            {
                if (isAsync)
                {
                    cleanupAsync();
                    tpe.shutdown();
                }
                throw dex;
            }
            catch (Exception ex)
            {
                if (isAsync)
                {
                    cleanupAsync();
                    tpe.shutdown();
                }
                ex.printStackTrace();
                throw new DENOPTIMException(ex);
            }
        }
        
        // Loop for creation of candidates until we have created enough new valid 
        // candidates or we have reached the max number of attempts.
        // WARNING: careful about the duplication of code in this loop and in 
        // the one above (with iterMolsToFragment)
        int i=0;
        List<Task> tasks = new ArrayList<>();
        try 
        {
            while (i < settings.getPopulationSize() *
                    settings.getMaxTriesFactor()) 
            {
                i++;
                
                if (stopped)
                {
                    break;
                }
                
                if (checkForException())
                {
                    stopRun();
                    throw new DENOPTIMException("Errors found during sub tasks "
                            + "execution.", ex);
                }
                
                synchronized (population)
                {
                    if (population.size() >= settings.getPopulationSize())
                        break;
                }
                
                Candidate candidate = EAUtils.buildCandidateFromScratch(mnt,
                        settings);
                
                i = processInitialPopCandidate(candidate, population, mnt, 
                        tasks, i, false, false);
            }
        } catch (DENOPTIMException dex)
        {
            if (isAsync)
            {
                cleanupAsync();
                tpe.shutdown();
            }
            throw dex;
        }
        catch (Exception ex)
        {
            if (isAsync)
            {
                cleanupAsync();
                tpe.shutdown();
            }
            ex.printStackTrace();
            throw new DENOPTIMException(ex);
        }
        
        mnt.printSummary();
 
        if (i >= (settings.getPopulationSize() * 
                settings.getMaxTriesFactor()))
        {
            if (isAsync)
            {
                cleanupCompleted();
                stopRun();
            }
            logger.log(Level.SEVERE,
                    "Unable to initialize population in {0} attempts."+NL, i);
 
            throw new DENOPTIMException("Unable to initialize population in " 
                    + i + " attempts (Population size: " + population.size() 
                    + ", tasks batch size: " + tasks.size() + ").");
        }
 
        synchronized (population)
        {
            // NB: this does not remove any item from the list
            population.trimToSize();
            Collections.sort(population, Collections.reverseOrder());
        }
    }
 
//------------------------------------------------------------------------------
    
    private int processInitialPopCandidate(Candidate candidate, 
            Population population, Monitor mnt,
            List<Task> batchOfSyncParallelTasks, int attemptsToFillBatch,
            boolean replaceWorstPopMember, boolean candidatesOverflow)
                    throws DENOPTIMException
    {
        if (candidate == null)
            return attemptsToFillBatch;
 
        candidate.setGeneration(0);
        
        if (((FitnessParameters)settings.getParameters(
                ParametersType.FIT_PARAMS)).checkPreFitnessUID())
        {
            try
            {
                if (!scs.addNewUniqueEntry(candidate.getUID()))
                {
                    mnt.increase(CounterID.DUPLICATEPREFITNESS);
                    return attemptsToFillBatch;
                }
            } catch (Exception e) {
                mnt.increase(CounterID.FAILEDDUPLICATEPREFITNESSDETECTION);
                return attemptsToFillBatch;
            }
        }
       
        OffspringEvaluationTask task = new OffspringEvaluationTask(
                settings,
                candidate, 
                null,
                EAUtils.getPathNameToGenerationFolder(0, settings), 
                population, mnt, settings.getUIDFileOut(),
                replaceWorstPopMember);
        
        // Submission is dependent on the parallelization scheme
        if (isAsync)
        {
            submitted.add(task);
            futures.put(task, tpe.submit(task));
            // We keep some memory but of previous tasks, but must
            // avoid memory leak due to storage of too many references 
            // to submitted tasks.
            if (submitted.size() > 2*settings.getNumberOfCPU())
            {
                cleanupCompleted();
            }
        } else {
            batchOfSyncParallelTasks.add(task);
            boolean submitBatch = false;
            if (!candidatesOverflow)
            {
                submitBatch = batchOfSyncParallelTasks.size() >= Math.abs(
                        population.size() - settings.getPopulationSize())
                        ||
                        //This to avoid the fixed batch size to block the
                        //generation of new candidates for too long
                        attemptsToFillBatch >= (0.1 * settings.getPopulationSize() *
                                settings.getMaxTriesFactor());
            } else {
                submitBatch = batchOfSyncParallelTasks.size() 
                        >= settings.getNumberOfCPU();
            }
            if (submitBatch)
            {
                // Now we have as many tasks as are needed to fill up the 
                // population or the batch.
                // Therefore we can run the execution service.
                // TasksBatchManager takes the collection of tasks and runs
                // them in batches of N according to the GA settings.
                submitSyncParallelBatch(batchOfSyncParallelTasks);
            } else {
                attemptsToFillBatch = 0;
            }
        }
        return attemptsToFillBatch;
    }
    
//------------------------------------------------------------------------------
    
    private void submitSyncParallelBatch(List<Task> batchOfSyncParallelTasks) 
            throws DENOPTIMException
    {
        tbm.executeTasks(batchOfSyncParallelTasks, 
                settings.getNumberOfCPU());
        batchOfSyncParallelTasks.clear();
    }
 
//------------------------------------------------------------------------------
 
    private boolean evolvePopulation(Population population, 
            int genId) throws DENOPTIMException
    {
        EAUtils.createFolderForGeneration(genId, settings);
        
        // Take a snapshot of the initial population members. This to exclude
        // that offsprings of this generation become parents in this generation.
        List<Candidate> eligibleParents = new ArrayList<Candidate>();
        int populationVersion = -1;
        int newPopSize = -1;
        synchronized (population)
        {
            for (Candidate c : population)
            {
                eligibleParents.add(c);
            }
            if (settings.parentsSurvive())
            {
                newPopSize = settings.getNumberOfChildren() 
                        + eligibleParents.size();
            } else {
                population.clear();
                newPopSize = settings.getPopulationSize();
            }
            populationVersion = population.getVersionID();
        }
        
        int i=0;
        List<Task> syncronisedTasks = new ArrayList<>();
        Monitor mnt = new Monitor("MonitorGen", genId, 
                settings.getMonitorFile(),settings.getMonitorDumpStep(), 
                settings.dumpMonitor(), settings.getLogger());
        try
        {
            while (i < settings.getPopulationSize() *
                    settings.getMaxTriesFactor()) 
            {
                i++;
                
                if (stopped)
                {
                    break;
                }
                
                if (checkForException())
                {
                    stopRun();
                    throw new DENOPTIMException("Errors found during sub-tasks "
                            + "execution.", ex);
                }
                
                synchronized (population)
                {
                    synchronized (candidatesToRemove)
                    {
                        if (candidatesToRemove.size()>0)
                        {
                            for (String id : candidatesToRemove)
                            {
                                Candidate c = population.getCandidateNamed(id);
                                if (c != null)
                                {
                                    population.remove(c);
                                    eligibleParents.remove(c);
                                }
                            }
                            candidatesToRemove.clear();
                        }
                    }
                }
                
                synchronized (population)
                {
                    if (population.size() >= newPopSize)
                        break;
                }
                
                File srcOfCandidate = null;
                List<Candidate> candidatesToEvaluate = new ArrayList<>();
                
                synchronized (candidatesToAdd)
                {
                    if (candidatesToAdd.size()>0)
                    {
                        srcOfCandidate = new File(candidatesToAdd.get(0));
                        candidatesToAdd.remove(0);
                        Candidate candidate = EAUtils.readCandidateFromFile(
                                srcOfCandidate, mnt, settings);
                        if (candidate == null)
                            continue;
                        else
                            candidatesToEvaluate.add(candidate);
                    }
                }
                
                if (candidatesToEvaluate.size()==0)
                {
                    if (settings.coupleMutationAndCrossover())
                    {
                        candidatesToEvaluate.addAll(makeOffspringB(
                                eligibleParents, population, mnt));
                    } else {    
                        candidatesToEvaluate.addAll(makeOffspringA(
                                eligibleParents, population, mnt));
                    }
                }
                if (candidatesToEvaluate.size()==0)
                    continue;
                
                // NB: for now we assume there can be up to two siblings
                for (int iSibling=0; iSibling<candidatesToEvaluate.size(); iSibling++)
                {
                    Candidate candidate = candidatesToEvaluate.get(iSibling);
                    int jSibling = 1;
                    if (iSibling==1)
                        jSibling = 0;
                    
                    Candidate sibling = null;
                    if (candidatesToEvaluate.size()>1)
                        sibling = candidatesToEvaluate.get(jSibling);
                    
                    candidate.setGeneration(genId);
                    
                    if (((FitnessParameters)settings.getParameters(
                            ParametersType.FIT_PARAMS)).checkPreFitnessUID())
                    {
                        try
                        {
                            if (!scs.addNewUniqueEntry(candidate.getUID()))
                            {
                                mnt.increase(CounterID.DUPLICATEPREFITNESS);
                                continue;
                            }
                        } catch (Exception e) {
                            mnt.increase(
                                    CounterID.FAILEDDUPLICATEPREFITNESSDETECTION);
                            continue;
                        }
                    }
                
                    OffspringEvaluationTask task = new OffspringEvaluationTask(
                            settings,
                            candidate,
                            sibling,
                            EAUtils.getPathNameToGenerationFolder(genId, settings), 
                            population, mnt, settings.getUIDFileOut(), false);
                    
                    if (isAsync)
                    {
                        submitted.add(task);
                        futures.put(task, tpe.submit(task));
                        // We keep some memory of previous tasks, but must
                        // avoid memory leak due to storage of too many references 
                        // to submitted tasks.
                        if (submitted.size() > 2*settings.getNumberOfCPU())
                        {
                            cleanupCompleted();
                        }
                    } else {
                        syncronisedTasks.add(task);
                        if (syncronisedTasks.size() 
                                >= Math.abs(population.size() - newPopSize)
                                ||
                                //This to avoid the fixed batch size to block the
                                //generation of new candidates for too long
                                i >= (0.1 * settings.getPopulationSize() *
                                        settings.getMaxTriesFactor()))
                        {
                            // Now we have as many tasks as are needed to fill up 
                            // the population, or we got sick to wait.
                            // TasksBatchManager takes the collection of tasks and
                            // runs them in batches of N, where N is given by the
                            // second argument.
                            submitSyncParallelBatch(syncronisedTasks);
                        }
                    }
                }
            }
        }
        catch (DENOPTIMException dex)
        {
            if (isAsync)
            {
                cleanupAsync();
                tpe.shutdown();
            }
            dex.printStackTrace();
            throw dex;
        }
        catch (Exception ex)
        {
            if (isAsync)
            {
                cleanupAsync();
                tpe.shutdown();
            }
            ex.printStackTrace();
            throw new DENOPTIMException(ex);
        }
        
        mnt.printSummary();
        
        if (i >= (settings.getPopulationSize() *
                settings.getMaxTriesFactor()))
        {
            if (isAsync)
            {
                cleanupCompleted();
                stopRun();
            }
            logger.log(Level.WARNING,
                    "Reached maximum number of attempts (" + i + ") to "
                    + "generate new candidates in generation " + genId + "." 
                            + NL);
        }
 
        // sort the population and trim it to size
        synchronized (population)
        {
            Collections.sort(population, Collections.reverseOrder());
            if (settings.getReplacementStrategy() == 1)
            {
                population.trim(settings.getPopulationSize());
            }
        }
        
        eligibleParents = null;
        syncronisedTasks.clear();
 
        // Check if the population has changed
        int newPopulationVersion = -1;
        synchronized (population)
        {
            newPopulationVersion = population.getVersionID();
        }
        
        return populationVersion != newPopulationVersion;
    }
    
//------------------------------------------------------------------------------
 
    @SuppressWarnings("incomplete-switch")
    private List<Candidate> makeOffspringA(List<Candidate> eligibleParents, 
            Population population, Monitor mnt) throws DENOPTIMException
    {
        CandidateSource src = EAUtils.chooseGenerationMethod(settings);
    
        List<Candidate> candidates = new ArrayList<Candidate>();
        switch (src)
        {
            // MANUAL is not a valid choice here
            case CROSSOVER:
            {
                candidates.addAll(EAUtils.buildCandidatesByXOver(
                        eligibleParents, population, mnt, settings));
                break;
            }
                
            case MUTATION:
            {
                Candidate candidate = EAUtils.buildCandidateByMutation(
                        eligibleParents, mnt, settings);
                if (candidate!=null)
                    candidates.add(candidate);
                break;
            }
                
            case CONSTRUCTION:
            {
                Candidate candidate = EAUtils.buildCandidateFromScratch(mnt,
                        settings);
                if (candidate!=null)
                    candidates.add(candidate);
                break;
            }
        }
        return candidates;
    }
    
//------------------------------------------------------------------------------
 
    @SuppressWarnings("incomplete-switch")
    private List<Candidate> makeOffspringB(List<Candidate> eligibleParents, 
            Population population, Monitor mnt) throws DENOPTIMException
    {
        CandidateSource src = EAUtils.pickNewCandidateGenerationMode(
                settings.getCrossoverWeight(), 
                settings.getMutationWeight(),
                settings.getConstructionWeight(),
                settings.getRandomizer());
    
        List<Candidate> candidates = new ArrayList<Candidate>();
        switch (src)
        {   
            case CROSSOVER:
            {
                candidates.addAll(EAUtils.buildCandidatesByXOver(
                        eligibleParents, population, mnt, settings));
                break;
            }
            
            case MUTATION:
            {
                List<Candidate> parents = EAUtils.buildCandidatesByXOver(
                        eligibleParents, population, mnt, settings);
                for (Candidate parent : parents)
                {
                    String provenanceMsg = parent.getGraph().getLocalMsg();
                    Candidate candidate = EAUtils.buildCandidateByMutation(
                            Arrays.asList(parent), mnt, settings);
                    if (candidate!=null)
                    {
                        candidate.getGraph().setLocalMsg("MutationOn" + 
                                provenanceMsg);
                        candidates.add(candidate);
                    }
                }
                break;
            }
                
            case CONSTRUCTION:
            {
                Candidate candidate = EAUtils.buildCandidateFromScratch(mnt,
                        settings);
                if (candidate!=null)
                    candidates.add(candidate);
                break;
            }
        }
        return candidates;
    }
 
//------------------------------------------------------------------------------
 
    public void stopRun()
    {
        if (isAsync)
        {
            cleanupAsync();
            tpe.shutdown();
        }
        stopped = true;
    }
    
//------------------------------------------------------------------------------
 
    private void cleanupAsync()
    {
        for (FitnessTask tsk: submitted)
        {
            tsk.stopTask();
        }
        for (FitnessTask tsk : futures.keySet())
        {
            futures.get(tsk).cancel(true);
        }
        futures.clear();
        submitted.clear();
        tpe.getQueue().clear();
    }
    
//------------------------------------------------------------------------------
 
    private void cleanupCompleted()
    {
        List<FitnessTask> completed = new ArrayList<FitnessTask>();
 
        for (FitnessTask t : submitted)
        {
            if (t.isCompleted())
                completed.add(t);
        }
 
        for (FitnessTask t : completed)
        {
            submitted.remove(t);
            futures.get(t).cancel(true);
            futures.remove(t);
        }
    }
 
//------------------------------------------------------------------------------
 
    private boolean checkForException()
    {
        boolean foundExceptions = false;
        if (isAsync)
        {
            for (FitnessTask tsk : submitted)
            {
                boolean interrupt = false;
                synchronized (tsk.lock)
                {
                    if (tsk.foundException())
                    {
                        foundExceptions = true;
                        logger.log(Level.SEVERE, "problems in " 
                          + tsk.toString() + ". ErrorMessage: '" 
                          + tsk.getErrorMessage() + "'. ExceptionInTask: "
                          + tsk.getException());
                        ex = tsk.getException().getCause();
                        interrupt = true;
                    }
                }
                if (interrupt)
                    break;
            }
        } else {
            // We don't really check of exceptions for synchronous scheme
            // because the executor service will detect the exception and stop
            // the experiment.
        }
        return foundExceptions;
    }
 
//------------------------------------------------------------------------------    
 
    public void removeCandidates(Set<String> candID)
    {
        synchronized (candidatesToRemove)
        {
            candidatesToRemove.addAll(candID);
        }
    }
    
//------------------------------------------------------------------------------    
 
    public void addCandidates(Set<String> pathNames)
    {
        synchronized (candidatesToAdd)
        {
            for (String pathName : pathNames)
            {
                if (!candidatesToAdd.contains(pathName))
                    candidatesToAdd.add(pathName);
            }
        }
    }
    
//------------------------------------------------------------------------------    
 
}