weka.experiment.RemoteExperiment Maven / Gradle / Ivy
/*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* RemoteExperiment.java
* Copyright (C) 2000 University of Waikato, Hamilton, New Zealand
*
*/
package weka.experiment;
import weka.core.FastVector;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Queue;
import weka.core.RevisionUtils;
import weka.core.SerializedObject;
import weka.core.Utils;
import weka.core.xml.KOML;
import weka.core.xml.XMLOptions;
import weka.experiment.xml.XMLExperiment;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.rmi.Naming;
import java.util.Enumeration;
import javax.swing.DefaultListModel;
/**
* Holds all the necessary configuration information for a distributed
* experiment. This object is able to be serialized for storage on disk.
*
* This class is experimental at present. Has been tested using
* CSVResultListener (sending results to standard out) and
* DatabaseResultListener (InstantDB + RmiJdbc bridge).
*
* Getting started:
*
* Start InstantDB (with the RMI bridge) on some machine. If using java2
* then specify -Djava.security.policy=db.policy to the
* virtual machine. Where db.policy is as follows:
*
* grant {
* permission java.security.AllPermission;
* };
*
*
* Start RemoteEngine servers on x machines as per the instructons in the
* README_Experiment_Gui file. There must be a
* DatabaseUtils.props in either the HOME or current directory of each
* machine, listing all necessary jdbc drivers.
*
* The machine where a RemoteExperiment is started must also have a copy
* of DatabaseUtils.props listing the URL to the machine where the
* database server is running (RmiJdbc + InstantDB).
*
* Here is an example of starting a RemoteExperiment:
*
*
*
* java -Djava.rmi.server.codebase=file:/path to weka classes/ \
* weka.experiment.RemoteExperiment -L 1 -U 10 \
* -T /home/ml/datasets/UCI/iris.arff \
* -D "weka.experiment.DatabaseResultListener" \
* -P "weka.experiment.RandomSplitResultProducer" \
* -h rosebud.cs.waikato.ac.nz -h blackbird.cs.waikato.ac.nz -r -- \
* -W weka.experiment.ClassifierSplitEvaluator -- \
* -W weka.classifiers.bayes.NaiveBayes
*
*
* The "codebase" property tells rmi where to serve up weka classes from.
* This can either be a file url (as long as a shared file system is being
* used that is accessable by the remoteEngine servers), or http url (which
* of course supposes that a web server is running and you have put your
* weka classes somewhere that is web accessable). If using a file url the
* trailing "/" is *most* important unless the weka classes are in a jar
* file.
*
* Valid options are:
*
* -L <num>
* The lower run number to start the experiment from.
* (default 1)
*
* -U <num>
* The upper run number to end the experiment at (inclusive).
* (default 10)
*
* -T <arff file>
* The dataset to run the experiment on.
* (required, may be specified multiple times)
*
* -P <class name>
* The full class name of a ResultProducer (required).
* eg: weka.experiment.RandomSplitResultProducer
*
* -D <class name>
* The full class name of a ResultListener (required).
* eg: weka.experiment.CSVResultListener
*
* -N <string>
* A string containing any notes about the experiment.
* (default none)
*
*
* Options specific to result producer weka.experiment.RandomSplitResultProducer:
*
*
* -P <percent>
* The percentage of instances to use for training.
* (default 66)
*
* -D
* Save raw split evaluator output.
*
* -O <file/directory name/path>
* The filename where raw output will be stored.
* If a directory name is specified then then individual
* outputs will be gzipped, otherwise all output will be
* zipped to the named file. Use in conjuction with -D. (default splitEvalutorOut.zip)
*
* -W <class name>
* The full class name of a SplitEvaluator.
* eg: weka.experiment.ClassifierSplitEvaluator
*
* -R
* Set when data is not to be randomized and the data sets' size.
* Is not to be determined via probabilistic rounding.
*
*
* Options specific to split evaluator weka.experiment.ClassifierSplitEvaluator:
*
*
* -W <class name>
* The full class name of the classifier.
* eg: weka.classifiers.bayes.NaiveBayes
*
* -C <index>
* The index of the class for which IR statistics
* are to be output. (default 1)
*
* -I <index>
* The index of an attribute to output in the
* results. This attribute should identify an
* instance in order to know which instances are
* in the test set of a cross validation. if 0
* no output (default 0).
*
* -P
* Add target and prediction columns to the result
* for each fold.
*
*
* Options specific to classifier weka.classifiers.rules.ZeroR:
*
*
* -D
* If set, classifier is run in debug mode and
* may output additional info to the console
*
*
* @author Mark Hall ([email protected])
* @version $Revision: 1.16 $
*/
public class RemoteExperiment
extends Experiment {
/** for serialization */
static final long serialVersionUID = -7357668825635314937L;
/** The list of objects listening for remote experiment events */
private FastVector m_listeners = new FastVector();
/** Holds the names of machines with remoteEngine servers running */
protected DefaultListModel m_remoteHosts = new DefaultListModel();
/** The queue of available hosts */
private Queue m_remoteHostsQueue = new Queue();
/** The status of each of the remote hosts */
private int [] m_remoteHostsStatus;
/** The number of times tasks have failed on each remote host */
private int [] m_remoteHostFailureCounts;
/** status of the remote host: available */
protected static final int AVAILABLE=0;
/** status of the remote host: in use */
protected static final int IN_USE=1;
/** status of the remote host: connection failed */
protected static final int CONNECTION_FAILED=2;
/** status of the remote host: some other failure */
protected static final int SOME_OTHER_FAILURE=3;
// protected static final int TO_BE_RUN=0;
// protected static final int PROCESSING=1;
// protected static final int FAILED=2;
// protected static final int FINISHED=3;
/** allow at most 3 failures on a host before it is removed from the list
of usable hosts */
protected static final int MAX_FAILURES=3;
/** Set to true if MAX_FAILURES exceeded on all hosts or connections fail
on all hosts or user aborts experiment (via gui) */
private boolean m_experimentAborted = false;
/** The number of hosts removed due to exceeding max failures */
private int m_removedHosts;
/** The count of failed sub-experiments */
private int m_failedCount;
/** The count of successfully completed sub-experiments */
private int m_finishedCount;
/** The base experiment to split up into sub experiments for remote
execution */
private Experiment m_baseExperiment = null;
/** The sub experiments */
protected Experiment [] m_subExperiments;
/** The queue of sub experiments waiting to be processed */
private Queue m_subExpQueue = new Queue();
/** The status of each of the sub-experiments */
protected int [] m_subExpComplete;
/**
* If true, then sub experiments are created on the basis of data sets
* rather than run number.
*/
protected boolean m_splitByDataSet = true;
/**
* Returns true if sub experiments are to be created on the basis of
* data set..
*
* @return a boolean value indicating whether sub
* experiments are to be created on the basis of data set (true) or
* run number (false).
*/
public boolean getSplitByDataSet() {
return m_splitByDataSet;
}
/**
* Set whether sub experiments are to be created on the basis of
* data set.
*
* @param sd true if sub experiments are to be created on the basis
* of data set. Otherwise sub experiments are created on the basis of
* run number.
*/
public void setSplitByDataSet(boolean sd) {
m_splitByDataSet = sd;
}
/**
* Construct a new RemoteExperiment using an empty Experiment as base
* Experiment
* @throws Exception if the base experiment is null
*/
public RemoteExperiment() throws Exception {
this(new Experiment());
}
/**
* Construct a new RemoteExperiment using a base Experiment
* @param base the base experiment to use
* @throws Exception if the base experiment is null
*/
public RemoteExperiment(Experiment base) throws Exception {
setBaseExperiment(base);
}
/**
* Add an object to the list of those interested in recieving update
* information from the RemoteExperiment
* @param r a listener
*/
public void addRemoteExperimentListener(RemoteExperimentListener r) {
m_listeners.addElement(r);
}
/**
* Get the base experiment used by this remote experiment
* @return the base experiment
*/
public Experiment getBaseExperiment() {
return m_baseExperiment;
}
/**
* Set the base experiment. A sub experiment will be created for each
* run in the base experiment.
* @param base the base experiment to use.
* @throws Exception if supplied base experiment is null
*/
public void setBaseExperiment(Experiment base) throws Exception {
if (base == null) {
throw new Exception("Base experiment is null!");
}
m_baseExperiment = base;
setRunLower(m_baseExperiment.getRunLower());
setRunUpper(m_baseExperiment.getRunUpper());
setResultListener(m_baseExperiment.getResultListener());
setResultProducer(m_baseExperiment.getResultProducer());
setDatasets(m_baseExperiment.getDatasets());
setUsePropertyIterator(m_baseExperiment.getUsePropertyIterator());
setPropertyPath(m_baseExperiment.getPropertyPath());
setPropertyArray(m_baseExperiment.getPropertyArray());
setNotes(m_baseExperiment.getNotes());
m_ClassFirst = m_baseExperiment.m_ClassFirst;
m_AdvanceDataSetFirst = m_baseExperiment.m_AdvanceDataSetFirst;
}
/**
* Set the user notes.
*
* @param newNotes New user notes.
*/
public void setNotes(String newNotes) {
super.setNotes(newNotes);
m_baseExperiment.setNotes(newNotes);
}
/**
* Set the lower run number for the experiment.
*
* @param newRunLower the lower run number for the experiment.
*/
public void setRunLower(int newRunLower) {
super.setRunLower(newRunLower);
m_baseExperiment.setRunLower(newRunLower);
}
/**
* Set the upper run number for the experiment.
*
* @param newRunUpper the upper run number for the experiment.
*/
public void setRunUpper(int newRunUpper) {
super.setRunUpper(newRunUpper);
m_baseExperiment.setRunUpper(newRunUpper);
}
/**
* Sets the result listener where results will be sent.
*
* @param newResultListener the result listener where results will be sent.
*/
public void setResultListener(ResultListener newResultListener) {
super.setResultListener(newResultListener);
m_baseExperiment.setResultListener(newResultListener);
}
/**
* Set the result producer used for the current experiment.
*
* @param newResultProducer result producer to use for the current
* experiment.
*/
public void setResultProducer(ResultProducer newResultProducer) {
super.setResultProducer(newResultProducer);
m_baseExperiment.setResultProducer(newResultProducer);
}
/**
* Set the datasets to use in the experiment
* @param ds the list of datasets to use
*/
public void setDatasets(DefaultListModel ds) {
super.setDatasets(ds);
m_baseExperiment.setDatasets(ds);
}
/**
* Sets whether the custom property iterator should be used.
*
* @param newUsePropertyIterator true if so
*/
public void setUsePropertyIterator(boolean newUsePropertyIterator) {
super.setUsePropertyIterator(newUsePropertyIterator);
m_baseExperiment.setUsePropertyIterator(newUsePropertyIterator);
}
/**
* Sets the path of properties taken to get to the custom property
* to iterate over.
*
* @param newPropertyPath an array of PropertyNodes
*/
public void setPropertyPath(PropertyNode [] newPropertyPath) {
super.setPropertyPath(newPropertyPath);
m_baseExperiment.setPropertyPath(newPropertyPath);
}
/**
* Sets the array of values to set the custom property to.
*
* @param newPropArray a value of type Object which should be an
* array of the appropriate values.
*/
public void setPropertyArray(Object newPropArray) {
super.setPropertyArray(newPropArray);
m_baseExperiment.setPropertyArray(newPropArray);
}
/**
* Prepares a remote experiment for running, creates sub experiments
*
* @throws Exception if an error occurs
*/
public void initialize() throws Exception {
if (m_baseExperiment == null) {
throw new Exception("No base experiment specified!");
}
m_experimentAborted = false;
m_finishedCount = 0;
m_failedCount = 0;
m_RunNumber = getRunLower();
m_DatasetNumber = 0;
m_PropertyNumber = 0;
m_CurrentProperty = -1;
m_CurrentInstances = null;
m_Finished = false;
if (m_remoteHosts.size() == 0) {
throw new Exception("No hosts specified!");
}
// initialize all remote hosts to available
m_remoteHostsStatus = new int [m_remoteHosts.size()];
m_remoteHostFailureCounts = new int [m_remoteHosts.size()];
m_remoteHostsQueue = new Queue();
// prime the hosts queue
for (int i=0;i 0) {
for (int i=0;i= 0) {
if (m_remoteHostFailureCounts[hostNum] < MAX_FAILURES) {
m_remoteHostsQueue.push(new Integer(hostNum));
} else {
notifyListeners(false,true,false,"Max failures exceeded for host "
+((String)m_remoteHosts.elementAt(hostNum))
+". Removed from host list.");
m_removedHosts++;
}
}
// check for all sub exp complete or all hosts failed or failed count
// exceeded
if (m_failedCount == (MAX_FAILURES * m_remoteHosts.size())) {
abortExperiment();
notifyListeners(false,true,true,"Experiment aborted! Max failures "
+"exceeded on all remote hosts.");
return;
}
if ((getSplitByDataSet() &&
(m_baseExperiment.getDatasets().size() == m_finishedCount)) ||
(!getSplitByDataSet() &&
((getRunUpper() - getRunLower() + 1) == m_finishedCount))) {
notifyListeners(false,true,false,"Experiment completed successfully.");
notifyListeners(false,true,true,postExperimentInfo());
return;
}
if (checkForAllFailedHosts()) {
return;
}
if (m_experimentAborted &&
(m_remoteHostsQueue.size() + m_removedHosts) == m_remoteHosts.size()) {
notifyListeners(false,true,true,"Experiment aborted. All remote tasks "
+"finished.");
}
if (!m_subExpQueue.empty() && !m_experimentAborted) {
if (!m_remoteHostsQueue.empty()) {
int availHost, waitingExp;
try {
availHost = ((Integer)m_remoteHostsQueue.pop()).intValue();
waitingExp = ((Integer)m_subExpQueue.pop()).intValue();
launchNext(waitingExp, availHost);
} catch (Exception ex) {
ex.printStackTrace();
}
}
}
}
/**
* Launch a sub experiment on a remote host
* @param wexp the index of the sub experiment to launch
* @param ah the index of the available host to launch on
*/
public void launchNext(final int wexp, final int ah) {
Thread subExpThread;
subExpThread = new Thread() {
public void run() {
m_remoteHostsStatus[ah] = IN_USE;
m_subExpComplete[wexp] = TaskStatusInfo.PROCESSING;
RemoteExperimentSubTask expSubTsk = new RemoteExperimentSubTask();
expSubTsk.setExperiment(m_subExperiments[wexp]);
String subTaskType = (getSplitByDataSet())
? "dataset :" + ((File)m_subExperiments[wexp].getDatasets().
elementAt(0)).getName()
: "run :" + m_subExperiments[wexp].getRunLower();
try {
String name = "//"
+((String)m_remoteHosts.elementAt(ah))
+"/RemoteEngine";
Compute comp = (Compute) Naming.lookup(name);
// assess the status of the sub-exp
notifyListeners(false,true,false,"Starting "
+subTaskType
+" on host "
+((String)m_remoteHosts.elementAt(ah)));
Object subTaskId = comp.executeTask(expSubTsk);
boolean finished = false;
TaskStatusInfo is = null;
while (!finished) {
try {
Thread.sleep(2000);
TaskStatusInfo cs = (TaskStatusInfo)comp.
checkStatus(subTaskId);
if (cs.getExecutionStatus() == TaskStatusInfo.FINISHED) {
// push host back onto queue and try launching any waiting
// sub-experiments
notifyListeners(false, true, false, cs.getStatusMessage());
m_remoteHostsStatus[ah] = AVAILABLE;
incrementFinished();
availableHost(ah);
finished = true;
} else if (cs.getExecutionStatus() == TaskStatusInfo.FAILED) {
// a non connection related error---possibly host doesn't have
// access to data sets or security policy is not set up
// correctly or classifier(s) failed for some reason
notifyListeners(false, true, false, cs.getStatusMessage());
m_remoteHostsStatus[ah] = SOME_OTHER_FAILURE;
m_subExpComplete[wexp] = TaskStatusInfo.FAILED;
notifyListeners(false,true,false,subTaskType
+" "+cs.getStatusMessage()
+". Scheduling for execution on another host.");
incrementFailed(ah);
// push experiment back onto queue
waitingExperiment(wexp);
// push host back onto queue and try launching any waiting
// sub-experiments. Host is pushed back on the queue as the
// failure may be temporary---eg. with InstantDB using the
// RMI bridge, two or more threads may try to create the
// experiment index or results table simultaneously; all but
// one will throw an exception. These hosts are still usable
// however.
availableHost(ah);
finished = true;
} else {
if (is == null) {
is = cs;
notifyListeners(false, true, false, cs.getStatusMessage());
} else {
if (cs.getStatusMessage().
compareTo(is.getStatusMessage()) != 0) {
notifyListeners(false, true, false,
cs.getStatusMessage());
}
is = cs;
}
}
} catch (InterruptedException ie) {
}
}
} catch (Exception ce) {
m_remoteHostsStatus[ah] = CONNECTION_FAILED;
m_subExpComplete[wexp] = TaskStatusInfo.TO_BE_RUN;
System.err.println(ce);
ce.printStackTrace();
notifyListeners(false,true,false,"Connection to "
+((String)m_remoteHosts.elementAt(ah))
+" failed. Scheduling "
+subTaskType
+" for execution on another host.");
checkForAllFailedHosts();
waitingExperiment(wexp);
} finally {
if (isInterrupted()) {
System.err.println("Sub exp Interupted!");
}
}
}
};
subExpThread.setPriority(Thread.MIN_PRIORITY);
subExpThread.start();
}
/**
* Overides the one in Experiment
* @throws Exception never throws an exception
*/
public void nextIteration() throws Exception {
}
/**
* overides the one in Experiment
*/
public void advanceCounters() {
}
/**
* overides the one in Experiment
*/
public void postProcess() {
}
/**
* Add a host name to the list of remote hosts
* @param hostname the host name to add to the list
*/
public void addRemoteHost(String hostname) {
m_remoteHosts.addElement(hostname);
}
/**
* Get the list of remote host names
* @return the list of remote host names
*/
public DefaultListModel getRemoteHosts() {
return m_remoteHosts;
}
/**
* Set the list of remote host names
* @param list the list of remote host names
*/
public void setRemoteHosts(DefaultListModel list) {
m_remoteHosts = list;
}
/**
* Overides toString in Experiment
* @return a description of this remote experiment
*/
public String toString() {
String result = m_baseExperiment.toString();
result += "\nRemote Hosts:\n";
for (int i=0;i\n"
+ "\tLoad experiment from file (default use cli options)\n"
+ "-s \n"
+ "\tSave experiment to file after setting other options\n"
+ "\t(default don't save)\n"
+ "-h \n"
+ "\tHost to run experiment on (may be specified more than once\n"
+ "\tfor multiple remote hosts)\n"
+ "-r \n"
+ "\tRun experiment on (default don't run)\n"
+ "-xml \n"
+ "\tget options from XML-Data instead from parameters\n"
+ "\n";
Enumeration enm = ((OptionHandler)base).listOptions();
while (enm.hasMoreElements()) {
Option option = (Option) enm.nextElement();
result += option.synopsis() + "\n";
result += option.description() + "\n";
}
throw new Exception(result + "\n" + ex.getMessage());
}
} else {
Object tmp;
// KOML?
if ( (KOML.isPresent()) && (expFile.toLowerCase().endsWith(KOML.FILE_EXTENSION)) ) {
tmp = KOML.read(expFile);
}
else
// XML?
if (expFile.toLowerCase().endsWith(".xml")) {
XMLExperiment xml = new XMLExperiment();
tmp = xml.read(expFile);
}
// binary
else {
FileInputStream fi = new FileInputStream(expFile);
ObjectInputStream oi = new ObjectInputStream(
new BufferedInputStream(fi));
tmp = oi.readObject();
oi.close();
}
if (tmp instanceof RemoteExperiment) {
exp = (RemoteExperiment)tmp;
} else {
base = (Experiment)tmp;
}
}
if (base != null) {
exp = new RemoteExperiment(base);
}
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