Adding the JavaEvA side of the matlab interface. Does not require external jmi.jar lib any more.
This commit is contained in:
Marcel Kronfeld
parent
2db50903f8
commit
ae0c66c212
146
src/javaeva/server/go/problems/MatlabEvalMediator.java
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146
src/javaeva/server/go/problems/MatlabEvalMediator.java
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package javaeva.server.go.problems;
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/**
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* This implements a thread acting as a mediator between JavaEvA and Matlab. Thanks to the idea
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* of Henning Schmidt!
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* As Java calling Matlab directly causes problems (due to Matlabs single-threadedness), Matlab
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* now starts a mediator thread which receives the data necessary to perform the evaluation in matlab
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* from the optimization thread. On receiving this "question" from the optimizer, the mediator thread
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* finishes, returning to Matlab and signaling that there is work to do.
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* However, the mediator object remains persistent, and the optimization thread keeps running
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* and waits for the mediator to signal that there is a result, which happens if Matlab calls setAnswer().
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* Then the optimizer thread resumes, while Matlab has to restart the mediator thread, so that it may
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* be informed about the next question, and so on. I havent checked how much performance is lost compared
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* to the earlier, asynchronous version, but it feels similar, a difference being that both cpu's
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* are now at 100% load, which is because two threads are running (and always at least waiting actively).
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* Adding sleep time reduces CPU load a lot but reduces efficiency badly at the same time, probably because
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* theres so much going on. For cases where the evaluation function is very time-consuming, adding sleep time
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* might be an option.
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*
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* @author mkron
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*
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*/
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public class MatlabEvalMediator implements Runnable {
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volatile boolean requesting = false;
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// final static boolean TRACE = false;
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volatile boolean fin = false;
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volatile double[] question = null;
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volatile double[] answer = null;
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volatile boolean quit = false;
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volatile double[] optSolution = null;
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volatile double[][] optSolSet = null;
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// MatlabProblem mp = null;
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// no good: even when waiting for only 1 ms the Matlab execution time increases by a factor of 5-10
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final static int sleepTime = 0;
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/**
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* Request evaluation from Matlab for the given params.
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*
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* @param x
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* @return
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*/
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double[] requestEval(MatlabProblem mp, double[] x) {
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// this.mp = mp;
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question = x;
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requesting = true;
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// int k=0;
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// mp.log("Requesting eval for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n");
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while (requesting && !quit) {
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// wait for matlab to answer the question
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if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
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// k++;
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// if (k>100) {
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// System.out.println("waiting for matlab to answer...");
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// k=0;
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// }
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}
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// mp.log("Requesting done \n");
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// matlab is finished, answer is here
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return getAnswer(); // return to JE with answer
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}
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/**
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* Wait loop, wait until the MatlabProblem requests an evaluation (or finishes), then return.
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*/
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public void run() {
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// int k=0;
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while (!requesting && !isFinished() && !quit) {
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// wait for JE to pose a question or finish all
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if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {};
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// k++;
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// if (k>100) {
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// System.out.println("waiting for JE to ask...");
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// k=0;
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// }
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}
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// mp.log("-- Request arrived in MP thread\n");
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// requesting is true, now finish and let Matlab work
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}
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/**
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* Cancel waiting in any case.
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*/
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public void quit() {
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quit = true;
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}
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/**
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* To be called from Matlab.
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* @return
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*/
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public double[] getQuestion() {
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// mp.log("-- Question: " + BeanInspector.toString(question) + "\n");
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return question;
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}
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double[] getAnswer() {
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return answer;
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}
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/**
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* To be called from Matlab giving the result of the question.
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*
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* @param y
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*/
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public void setAnswer(double[] y) {
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// mp.log("-- setAnswer: " + BeanInspector.toString(y) + "\n");
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answer = y;
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requesting = false; // answer is finished, break request loop
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}
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void setFinished(boolean val) {
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fin = val;
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}
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/**
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* To be called from Matlab signalling when optimizaton is completely finished.
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* @return
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*/
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public boolean isFinished() {
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return fin;
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}
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void setSolution(double[] sol) {
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optSolution = sol;
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}
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void setSolutionSet(double[][] solSet) {
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optSolSet = solSet;
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}
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/**
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* Matlab may retrieve result.
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* @return
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*/
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public double[] getSolution() {
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return optSolution;
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}
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/**
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* Matlab may retrieve result.
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* @return
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*/
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public double[][] getSolutionSet() {
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return optSolSet;
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}
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}
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453
src/javaeva/server/go/problems/MatlabProblem.java
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453
src/javaeva/server/go/problems/MatlabProblem.java
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package javaeva.server.go.problems;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.PrintStream;
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import java.io.PrintWriter;
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import java.io.Serializable;
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import java.io.StringWriter;
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import javaeva.OptimizerFactory;
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import javaeva.OptimizerRunnable;
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import javaeva.gui.BeanInspector;
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import javaeva.server.go.individuals.AbstractEAIndividual;
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import javaeva.server.go.individuals.ESIndividualDoubleData;
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import javaeva.server.go.individuals.InterfaceDataTypeDouble;
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import javaeva.server.go.operators.distancemetric.PhenotypeMetric;
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import javaeva.server.go.operators.postprocess.InterfacePostProcessParams;
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import javaeva.server.go.operators.postprocess.PostProcess;
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import javaeva.server.go.operators.postprocess.PostProcessParams;
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import javaeva.server.go.populations.Population;
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import javaeva.server.go.strategies.InterfaceOptimizer;
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import javaeva.server.stat.InterfaceTextListener;
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public class MatlabProblem extends AbstractProblemDouble implements InterfaceTextListener, Serializable {
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private static final long serialVersionUID = 4913310869887420815L;
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public static final boolean TRACE = false;
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// transient protected Matlab matlab = null;
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transient OptimizerRunnable runnable = null;
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protected boolean allowSingleRunnable = true;
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// protected String jmInterface;
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protected int problemDimension = 10;
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transient PrintStream dos = null;
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protected double[][] range = null;
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private static final String defTestOut = "matlabproblem-testout.dat";
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boolean forwardStatisticsOutput = false;
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private MatlabEvalMediator handler = null;
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private F1Problem f1 = new F1Problem(); // TODO
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// transient private double[] currArray = null;
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// private String mtCmd = null;
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public MatlabProblem(MatlabProblem o) {
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// this.matlab = o.matlab;
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this.handler = o.handler;
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this.runnable = o.runnable;
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this.allowSingleRunnable = o.allowSingleRunnable;
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// this.jmInterface = new String(o.jmInterface);
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this.problemDimension = o.problemDimension;
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// this.res = new ResultArr();
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// if (o.res != null) if (o.res.get() != null) res.set(o.res.get());
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this.range = o.makeRange();
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// this.mtCmd = o.mtCmd;
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// currArray = null;
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}
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public Object clone() {
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return new MatlabProblem(this);
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}
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public MatlabProblem(String nameJEInterface, int dim) {
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this(nameJEInterface, dim, null);
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range = super.makeRange();
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}
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public MatlabProblem(String nameJEInterface, int dim, double[][] range) {
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init(nameJEInterface, dim, range, defTestOut);
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}
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public MatlabProblem(String nameJEInterface, int dim, double lower, double upper) {
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this(nameJEInterface, dim, null);
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double[][] range = new double[dim][2];
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for (int i=0; i<dim; i++) {
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range[dim][0] = lower;
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range[dim][1] = upper;
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}
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}
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public void setMediator(MatlabEvalMediator h) {
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handler = h;
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}
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public void initProblem() {
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init(/*this.jmInterface*/ null, this.problemDimension, this.range, defTestOut);
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}
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private void init(String nameJEInterface, int dim, double[][] rng, String outFile) {
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problemDimension = dim;
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if ((rng != null) && (dim != rng.length)) throw new ArrayIndexOutOfBoundsException("Mismatching dimension and range!");
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range = rng;
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initTemplate();
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// res = new ResultArr();
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if ((dos == null) && TRACE) {
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try {
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dos = new PrintStream(new FileOutputStream(outFile));
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} catch (FileNotFoundException e) {
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e.printStackTrace();
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}
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}
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log("range is " + BeanInspector.toString(range)+ "\n");
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log("template len: " + ((ESIndividualDoubleData)m_Template).getDGenotype().length + "\n");
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try {
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// if (matlab == null)
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// matlab = new Matlab();//this command links to the current matlab session
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// try {
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// matlab.eval("JE='hello'");
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// } catch (Exception e) {
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// e.printStackTrace();
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// }
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} catch (Error e) {
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log("Error: " + e.toString());
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System.err.println("Error: could not create MatlabProblem instance. MatlabProblem can only be used from Matlab.");
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}
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// this.jmInterface = nameJEInterface;
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// mtCmd = new String("evaluateJE("+jmInterface+")");
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}
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// /**
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// * @return the jmInterface
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// */
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// public String getJmInterfaceName() {
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// return jmInterface;
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// }
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// /**
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// * @param jmInterface the jmInterface to set
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// */
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// public void setJmInterfaceName(String jmInterface) {
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// this.jmInterface = jmInterface;
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// }
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public void setStatsOutput(boolean forwardStats) {
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forwardStatisticsOutput = forwardStats;
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}
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public String jmiInterfaceNameTipText() {
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return "Name of the JEInterface instance in Matlab";
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}
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/**
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* @param problemDimension the problemDimension to set
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*/
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public void setProblemDimension(int problemDimension) {
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this.problemDimension = problemDimension;
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}
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public int getProblemDimension() {
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return problemDimension;
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}
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public String problemDimensionTipTex() {
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return "The dimension of the problem.";
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}
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protected double[][] makeRange() {
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if (range==null) range=super.makeRange();
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return range;
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}
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protected double getRangeLowerBound(int dim) {
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return (range==null) ? super.getRangeLowerBound(dim) : range[dim][0];
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}
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protected double getRangeUpperBound(int dim) {
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return (range==null) ? super.getRangeUpperBound(dim) : range[dim][1];
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}
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// public double[] getCurrentDoubleArray() {
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// return currArray;
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// }
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//
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// public double[] getNewDoubleArray() {
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// currArray = new double[problemDimension];
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// for (int i=0; i<problemDimension; i++) currArray[i] = RandomNumberGenerator.gaussianDouble(1);
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// return currArray;
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// }
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public void log(String str) {
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if (dos != null) {
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dos.print((String)str);
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dos.flush();
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}
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}
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public double[] eval(double[] x) {
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log("evaluating " + BeanInspector.toString(x) + "\n");
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double[] res = handler.requestEval(this, x);
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double diff = PhenotypeMetric.euclidianDistance(res, f1.eval(x));
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log("result: " + BeanInspector.toString(res) + " compared to " + BeanInspector.toString(f1.eval(x)) + "\n");
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if (diff != 0) {
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log("!!! diff is " + diff + "\n");
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}
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return res;
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// synchronized (this) {
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// try {
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// res.reset();
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// currArray = x;
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// log("evaluating " + BeanInspector.toString(x) + "\n");
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// matlab.eval(mtCmd, (CompletionObserver)this);
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// this.wait();
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// } catch (InterruptedException e) {
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// log("wait interrupted: " + e.getMessage() + " \n");
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// }
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// }
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// log("wait done, returning " + res.get()[0] + " \n");
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// return res.get();
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}
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public void optimize(final int optType, String outputFilePrefix) {
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optimize(optType, outputFilePrefix, null, null);
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}
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public void optimize(final int optType, String outputFilePrefix, Object[] specParams, Object[] specValues) {
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if (allowSingleRunnable && (runnable != null) && (!runnable.isFinished())) {
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System.err.println("Please wait for the current optimization to finish");
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} else {
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handler.setFinished(false);
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runnable = OptimizerFactory.getOptRunnable(optType, (AbstractOptimizationProblem)this, outputFilePrefix);
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// runnable.getGOParams().setPostProcessParams(new PostProcessParams(0, 0.01, 5));
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runnable.setTextListener(this);
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if ((specParams != null) && (specParams.length > 0)) {
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if ((specValues == null) || (specValues.length != specParams.length)) {
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System.err.println("mismatching value list for parameter arguments: " + specValues);
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} else {
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log("setting specific parameters...\n");
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InterfaceOptimizer opt = runnable.getGOParams().getOptimizer();
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for (int i=0; i<specParams.length; i++) { // loop over settings
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log("try setting " + specParams[i] + " to " + specValues[i]);
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if (!BeanInspector.setMem(opt, (String)specParams[i], specValues[i])) {
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log("... Fail!\n");
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System.err.println("Unable to set parameter " + specParams[i] + ", skipping...");
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||||||
|
} else log("... Ok.\n");
|
||||||
|
}
|
||||||
|
log(BeanInspector.toString(BeanInspector.getMemberDescriptions(opt, true)));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
new Thread(new WaitForEvARunnable(runnable, this)).start();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void startPostProcess(InterfacePostProcessParams ppp) {
|
||||||
|
if (ppp.isDoPostProcessing()) {
|
||||||
|
if (allowSingleRunnable && (runnable != null) && (!runnable.isFinished())) {
|
||||||
|
System.err.println("Please wait for the current optimization to finish");
|
||||||
|
} else {
|
||||||
|
handler.setFinished(false);
|
||||||
|
log("\nstarting post process thread... " + BeanInspector.toString(ppp));
|
||||||
|
// runnable.setTextListener(this);
|
||||||
|
runnable.setDoRestart(true);
|
||||||
|
runnable.setDoPostProcessOnly(true);
|
||||||
|
runnable.setPostProcessingParams(ppp);
|
||||||
|
// runnable.restartOpt();
|
||||||
|
// log("\nppp are " + BeanInspector.toString(runnable.getGOParams().getPostProcessParams()));
|
||||||
|
new Thread(new WaitForEvARunnable(runnable, this)).start();
|
||||||
|
}
|
||||||
|
} else System.err.println("Nothing to be done.");
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Request post processing of the last optimization results with given parameters
|
||||||
|
* and export the result solution set to matlab.
|
||||||
|
*
|
||||||
|
* @param steps post processing steps with hill climber
|
||||||
|
* @param sigma sigma parameter for clustering
|
||||||
|
* @param nBest maximum number of solutions to retrieve
|
||||||
|
*/
|
||||||
|
public void requestPostProcessing(int steps, double sigma, int nBest) {
|
||||||
|
PostProcessParams ppp = new PostProcessParams(steps, sigma, nBest);
|
||||||
|
startPostProcess(ppp);
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Request post processing of the last optimization results with given parameters
|
||||||
|
* and export the result solution set to matlab.
|
||||||
|
* This variant retrieves all solutions found in this way.
|
||||||
|
*
|
||||||
|
* @param steps post processing steps with hill climber
|
||||||
|
* @param sigma sigma parameter for clustering
|
||||||
|
*/
|
||||||
|
public void requestPostProcessing(int steps, double sigma) {
|
||||||
|
requestPostProcessing(steps, sigma, -1);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void stopOptimize() {
|
||||||
|
log(">>>>>>>>>> Stop event!\n");
|
||||||
|
if (runnable != null) {
|
||||||
|
runnable.stopOpt();
|
||||||
|
}
|
||||||
|
PostProcess.stopHC();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getInfoString() {
|
||||||
|
if (runnable == null) return "";
|
||||||
|
StringBuffer sb = new StringBuffer("");
|
||||||
|
sb.append(runnable.terminatedBecause());
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getFunctionCalls() {
|
||||||
|
if (runnable == null) return 0;
|
||||||
|
return runnable.getGOParams().getOptimizer().getPopulation().getFunctionCalls();
|
||||||
|
}
|
||||||
|
//
|
||||||
|
// Matlab getMatlab() {
|
||||||
|
// return matlab;
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
void exportResultPopulationToMatlab(Population pop) {
|
||||||
|
double[][] solSet;
|
||||||
|
|
||||||
|
if ((pop != null) && (pop.size()>0)) {
|
||||||
|
solSet = new double[pop.size()][];
|
||||||
|
for (int i=0; i<pop.size(); i++) {
|
||||||
|
solSet[i]=((InterfaceDataTypeDouble)pop.getEAIndividual(i)).getDoubleData();
|
||||||
|
}
|
||||||
|
handler.setSolutionSet(solSet);
|
||||||
|
} else {
|
||||||
|
handler.setSolutionSet(null);
|
||||||
|
}
|
||||||
|
// String resStr;
|
||||||
|
// if ((pop == null) || (pop.size() == 0)) resStr = "[]";
|
||||||
|
// else {
|
||||||
|
// StringBuffer sb = new StringBuffer();
|
||||||
|
// sb.append("[");
|
||||||
|
// for (int i=0; i<pop.size(); i++) {
|
||||||
|
// sb.append(AbstractEAIndividual.getDefaultDataString(pop.getEAIndividual(i), " "));
|
||||||
|
// if (i<pop.size()-1) sb.append(";");
|
||||||
|
// }
|
||||||
|
// sb.append("]");
|
||||||
|
// resStr = sb.toString();
|
||||||
|
// }
|
||||||
|
// log("result array was " + resStr + "\n");
|
||||||
|
// try {
|
||||||
|
// String cmd = jmInterface + "= setResultArrayJE(" + jmInterface + ", " + resStr + ")";
|
||||||
|
// log("trying cmd: "+ cmd + "\n");
|
||||||
|
// matlab.eval(cmd);
|
||||||
|
// } catch (Exception e) {
|
||||||
|
// log("Exception when exporting result to Matlab! "+e.getMessage());
|
||||||
|
// }
|
||||||
|
}
|
||||||
|
|
||||||
|
void exportResultToMatlab(double[] result) {
|
||||||
|
handler.setSolution(result);
|
||||||
|
// String resStr;
|
||||||
|
// if (result == null) resStr = "[]";
|
||||||
|
// else resStr = BeanInspector.toString(result);
|
||||||
|
// log("result was " + resStr + "\n");
|
||||||
|
// try {
|
||||||
|
// String cmd = jmInterface + "= setResultJE(" + jmInterface + ", " + resStr + ")";
|
||||||
|
// log("trying cmd: "+ cmd + "\n");
|
||||||
|
// matlab.eval(cmd);
|
||||||
|
// } catch (Exception e) {
|
||||||
|
// log("Exception when exporting result to Matlab! "+e.getMessage());
|
||||||
|
// }
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* To be called by the executing thread to inform that the thread is finished.
|
||||||
|
* We
|
||||||
|
*/
|
||||||
|
void notifyFinished() {
|
||||||
|
handler.setFinished(true);
|
||||||
|
}
|
||||||
|
|
||||||
|
public double[] getIntermediateResult() {
|
||||||
|
if (runnable == null) return null;
|
||||||
|
else return runnable.getDoubleSolution();
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Return the number of function calls performed so far.
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
public int getProgress() {
|
||||||
|
if (runnable == null) return 0;
|
||||||
|
else return runnable.getProgress();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String globalInfo() {
|
||||||
|
return "Interface problem class for optimization in Matlab, only usable from within Matlab";
|
||||||
|
}
|
||||||
|
|
||||||
|
public void print(String str) {
|
||||||
|
if (forwardStatisticsOutput) {
|
||||||
|
// matlab displays sysout output in the command window, so we simply use this channel
|
||||||
|
System.out.print(str);
|
||||||
|
}
|
||||||
|
log(str);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void println(String str) {
|
||||||
|
print(str);
|
||||||
|
print("\n");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
////////////////////////////
|
||||||
|
|
||||||
|
class WaitForEvARunnable implements Runnable {
|
||||||
|
OptimizerRunnable runnable;
|
||||||
|
MatlabProblem mp;
|
||||||
|
|
||||||
|
public WaitForEvARunnable(OptimizerRunnable runnable, MatlabProblem mp) {
|
||||||
|
this.runnable = runnable;
|
||||||
|
this.mp = mp;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void run() {
|
||||||
|
if (runnable != null) {
|
||||||
|
mp.log("\nStarting optimize runnable!\n");
|
||||||
|
|
||||||
|
synchronized (runnable) {
|
||||||
|
try {
|
||||||
|
// whole optimization thread goes in here
|
||||||
|
new Thread(runnable).start();
|
||||||
|
mp.log("Starting optimize thread done!\n");
|
||||||
|
runnable.wait();
|
||||||
|
// wait for the runnable to finish
|
||||||
|
mp.log("After wait!\n");
|
||||||
|
} catch (InterruptedException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
mp.log("WaitForEvARunnable was interrupted with " + e.getMessage());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
try {
|
||||||
|
mp.log("runnable.getSolution: " + BeanInspector.toString(runnable.getDoubleSolution()));
|
||||||
|
mp.log("\ngetAllSols best: " + AbstractEAIndividual.getDefaultDataString(runnable.getGOParams().getOptimizer().getAllSolutions().getBestEAIndividual()));
|
||||||
|
mp.log("\n");
|
||||||
|
// write results back to matlab
|
||||||
|
mp.exportResultToMatlab(runnable.getDoubleSolution());
|
||||||
|
mp.exportResultPopulationToMatlab(runnable.getSolutionSet());
|
||||||
|
System.out.println("Optimization finished: " + mp.getInfoString());
|
||||||
|
} catch (Exception e) {
|
||||||
|
StringWriter sw = new StringWriter();
|
||||||
|
e.printStackTrace(new PrintWriter(sw));
|
||||||
|
mp.log("error in callback: " + e.getMessage() + " " + sw.toString() + "\n");
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
System.err.println("Invalid optimization call.");
|
||||||
|
mp.log("invalid call, no optimization started.\n");
|
||||||
|
mp.exportResultToMatlab(null);
|
||||||
|
mp.exportResultPopulationToMatlab(null);
|
||||||
|
}
|
||||||
|
mp.notifyFinished();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
x
Reference in New Issue
Block a user