r3893 - in branches/4.0.1: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/aspect src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/equation src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/ui/input src/main/java/fr/ifremer/isisfish/util src/main/resources src/main/resources/i18n src/main/resources/templates/ssh - Isis-fish-commits

19 Mar 2014

Author: echatellier
Date: 2014-03-19 10:51:00 +0100 (Wed, 19 Mar 2014)
New Revision: 3893

Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/3893

Log:
Merge trunk@3892 into branch 4.0.1@3890

Added:
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCache.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java
Removed:
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java
Modified:
   branches/4.0.1/
   branches/4.0.1/pom.xml
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/equation/PopulationGrowth.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx
   branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx
   branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties
   branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties
   branches/4.0.1/src/main/resources/sensitivity.properties
   branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl


Property changes on: branches/4.0.1
___________________________________________________________________
Modified: svn:mergeinfo
   - /branches/4.0.0-svnkit:3665-3698
/branches/4.1:3601-3670
/trunk:3616-3799
   + /branches/4.0.0-svnkit:3665-3698
/branches/4.1:3601-3670
/trunk:3616-3892

Modified: branches/4.0.1/pom.xml
===================================================================

--- branches/4.0.1/pom.xml	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/pom.xml	2014-03-19 09:51:00 UTC (rev 3893)
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.nuiton</groupId>
         <artifactId>mavenpom4redmine</artifactId>
-        <version>4.7</version>
+        <version>5.0.1</version>
     </parent>
 
     <groupId>fr.ifremer</groupId>
@@ -345,6 +345,12 @@
             <scope>compile</scope>
         </dependency>
 
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>16.0.1</version>
+        </dependency>
+
         <!-- Tests -->
         <dependency>
             <groupId>junit</groupId>
@@ -359,7 +365,7 @@
     <description>Simulateur de pecherie complexe.</description>
     <inceptionYear>1999</inceptionYear>
 
-    <url>http://maven-site.forge.codelutin.com/isis-fish</url>
+    <url>http://doc.codelutin.com/isis-fish</url>
 
     <organization>
         <name>CodeLutin</name>
@@ -405,7 +411,7 @@
 
     <ciManagement>
         <system>hudson</system>
-        <url>http://jenkins.forge.codelutin.com/jenkins/job/isis-fish</url>
+        <url>http://ci.codelutin.com/jenkins/job/isis-fish-ci</url>
     </ciManagement>
 
     <developers>
@@ -441,26 +447,28 @@
             <timezone>+2</timezone>
         </developer>
         <developer>
-            <id>sletellier</id>
-            <name>Sylvain Letellier</name>
-            <email>letellier@codelutin.com</email>
+            <id>jcouteau</id>
+            <name>Jean Couteau</name>
+            <email>couteau@codelutin.com</email>
             <organization>CodeLutin</organization>
             <roles>
                 <role>Développeur</role>
             </roles>
             <timezone>+2</timezone>
         </developer>
-        <developer>
-            <id>jcouteau</id>
-            <name>Jean Couteau</name>
-            <email>couteau@codelutin.com</email>
+    </developers>
+
+    <contributors>
+        <contributor>
+            <name>Sylvain Letellier</name>
+            <email>letellier@codelutin.com</email>
             <organization>CodeLutin</organization>
             <roles>
                 <role>Développeur</role>
             </roles>
             <timezone>+2</timezone>
-        </developer>
-    </developers>
+        </contributor>
+    </contributors>
 
     <!-- ************************************************************* -->
     <!-- *** Build Settings ****************************************** -->
@@ -470,7 +478,7 @@
     <properties>
         <!-- Super pom properties -->
         <projectId>isis-fish</projectId>
-        <platform>forge.codelutin.com</platform>
+        <platform>codelutin.com</platform>
         <siteLocales>fr,en</siteLocales>
         <maven.jar.main.class>fr.ifremer.isisfish.IsisFish</maven.jar.main.class>
         <license.licenseName>gpl_v3</license.licenseName>
@@ -501,7 +509,7 @@
 
     <distributionManagement>
         <site>
-            <id>${platform}</id>
+            <id>doc.${platform}</id>
             <url>${our.site.repository}/isis-fish</url>
         </site>
     </distributionManagement>
@@ -667,9 +675,9 @@
     <!-- *** Build Environment ************************************** -->
     <!-- ************************************************************* -->
     <scm>
-        <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/branches/4.0.1</connection>
-        <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/branches/4.0.1</developerConnection>
-        <url>http://svn.forge.codelutin.com/svn/isis-fish/branches/4.0.1</url>
+        <connection>scm:svn:http://svn.codelutin.com/isis-fish/branches/4.0.1</connection>
+        <developerConnection>scm:svn:http://svn.codelutin.com/isis-fish/branches/4.0.1</developerConnection>
+        <url>http://svn.codelutin.com/isis-fish/branches/4.0.1</url>
     </scm>
 
     <repositories>
@@ -708,6 +716,7 @@
                                 <descriptor>src/main/assembly/bin.xml</descriptor>
                             </descriptors>
                             <attach>false</attach>
+                            <recompressZippedFiles>true</recompressZippedFiles>
                         </configuration>
                         <executions>
                             <execution>

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisConfig.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -59,6 +59,8 @@
 import fr.ifremer.isisfish.simulator.launcher.SSHSimulatorLauncher;
 import fr.ifremer.isisfish.simulator.launcher.SimulationService;
 import fr.ifremer.isisfish.simulator.launcher.SubProcessSimulationLauncher;
+import fr.ifremer.isisfish.util.IsisCacheBackend;
+import fr.ifremer.isisfish.util.IsisCacheBackendOnGuava;
 import fr.ifremer.isisfish.vcs.VCS;
 
 /**
@@ -929,7 +931,7 @@
     /**
      * L'implementation de la class gérant les implémentations de vecteur de
      * matrice pour les fichiers mappés.
-     * 
+     *
      * @return
      * @since 4.2.1.1
      */
@@ -938,6 +940,18 @@
         return result;
     }
 
+    /**
+     * Retourne la factory a utilise pour le cache
+     *
+     * @return factory a utilise pour le backend de cache
+     * @since 4.2.1.2
+     */
+    public IsisCacheBackend.Factory getCacheBackendFactoryClass() {
+        IsisCacheBackend.Factory result = getOptionAsObject(
+                IsisCacheBackend.Factory.class, Option.CACHE_BACKEND_FACTORY_CLASS.key);
+        return result;
+    }
+
     //////////////////////////////////////////////////
     // Toutes les options disponibles
     //////////////////////////////////////////////////
@@ -1044,7 +1058,8 @@
         USER_NAME("user.name", n_("isisfish.config.main.userName.description"), System.getProperty("user.name")),
         SMTP_SERVER("smtpServer", n_("isisfish.config.main.smtpServer.description"), "smtp"),
         USER_MAIL("userMail", n_("isisfish.config.main.userMail.description"), USER_NAME.key + "@" + VCS_HOST_NAME.key),
-        MAPPED_RESULT_MATRIX_VECTOR_CLASS("mapped.result.matrix.vector.class", n_("isisfish.config.mapped.result.matrix.vector.class.description"), DoubleBigVector.class.getName());
+        MAPPED_RESULT_MATRIX_VECTOR_CLASS("mapped.result.matrix.vector.class", n_("isisfish.config.mapped.result.matrix.vector.class.description"), DoubleBigVector.class.getName()),
+        CACHE_BACKEND_FACTORY_CLASS("cache.backend.factory.class", n_("isisfish.config.cache.backend.factory.class.description"), IsisCacheBackendOnGuava.IsisCacheBackendOnGuavaFactory.class.getName());
 
         public String key;
         public String description;

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/IsisFish.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -44,6 +44,7 @@
 import javax.swing.JOptionPane;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 import javax.swing.UnsupportedLookAndFeelException;
 
@@ -73,10 +74,12 @@
 import fr.ifremer.isisfish.datastore.SimulationPlanStorage;
 import fr.ifremer.isisfish.datastore.SimulationStorage;
 import fr.ifremer.isisfish.datastore.SimulatorStorage;
+import fr.ifremer.isisfish.simulator.launcher.SimulationMonitor;
 import fr.ifremer.isisfish.simulator.launcher.SimulationService;
 import fr.ifremer.isisfish.ui.WelcomeTabUI;
 import fr.ifremer.isisfish.ui.WelcomeUI;
 import fr.ifremer.isisfish.ui.util.ErrorHelper;
+import fr.ifremer.isisfish.util.IsisCache;
 import fr.ifremer.isisfish.util.IsisMatrixSemanticMapper;
 import fr.ifremer.isisfish.vcs.VCS;
 import fr.ifremer.isisfish.vcs.VCSActionEvent;
@@ -243,6 +246,9 @@
             I18n.init(new ClassPathI18nInitializer(), config.getLocale());
         }
 
+        // init cache backend
+        IsisCache.defaultFactory = config.getCacheBackendFactoryClass();
+
         // after init shutdown hook
         Runtime.getRuntime().addShutdownHook(new IsisQuitHook());
     }
@@ -631,97 +637,112 @@
     public static void launchUI() {
         if (config.isLaunchUI()) {
             
-            // catch wall application exception
-            Thread.setDefaultUncaughtExceptionHandler(new Thread.UncaughtExceptionHandler() {
-                public void uncaughtException(Thread t, Throwable cause) {
-                    if (cause instanceof LinkageError) {
-                        if (log.isFatalEnabled()) {
-                            log.fatal("Linkage error detected", cause);
-                        }
+            SwingUtilities.invokeLater(new Runnable() {
+                @Override
+                public void run() {
 
-                        // a real java.lang.Error sometimes happen when
-                        // using non recompiled script due to dependency changes
-                        // this is the better solution found :
-                        // remove isis build directory
-                        //FileUtils.deleteQuietly(IsisFish.config.getCompileDirectory());
+                    // catch wall application exception
+                    Thread.setDefaultUncaughtExceptionHandler(new Thread.UncaughtExceptionHandler() {
+                        public void uncaughtException(Thread t, Throwable cause) {
+                            if (cause instanceof LinkageError) {
+                                if (log.isFatalEnabled()) {
+                                    log.fatal("Linkage error detected", cause);
+                                }
+        
+                                // a real java.lang.Error sometimes happen when
+                                // using non recompiled script due to dependency changes
+                                // this is the better solution found :
+                                // remove isis build directory
+                                try {
+                                    FileUtils.deleteDirectory(IsisFish.config.getCompileDirectory());
+                                } catch (IOException e) {
+                                    // TODO Auto-generated catch block
+                                    e.printStackTrace();
+                                }
 
-                        ErrorHelper.showErrorDialog(null, _("isisfish.error.linkageerror.message"), cause);
-                    }
-                    else {
-                        if (log.isErrorEnabled()) {
-                            log.error("Global application exception", cause);
+                                ErrorHelper.showErrorDialog(null, _("isisfish.error.linkageerror.message"), cause);
+                            }
+                            else {
+                                if (log.isErrorEnabled()) {
+                                    log.error("Global application exception", cause);
+                                }
+        
+                                // les NumberFormatException sont courantes lors de la saisie
+                                // ca va etre relou de toutes les afficher
+                                Throwable lastCause = cause;
+                                while (lastCause.getCause() != null) {
+                                    lastCause = lastCause.getCause();
+                                }
+                                if (!(lastCause instanceof NumberFormatException)) {
+                                    ErrorHelper.showErrorDialog(null, cause.getMessage(), cause);
+                                }
+                            }
                         }
-
-                        // les NumberFormatException sont courantes lors de la saisie
-                        // ca va etre relou de toutes les afficher
-                        Throwable lastCause = cause;
-                        while (lastCause.getCause() != null) {
-                            lastCause = lastCause.getCause();
+                    });
+        
+                    // init simulater manager
+                    SimulationService.getService();
+        
+                    // init IsisTray
+                    IsisTray.getInstance();
+        
+                    // OpenMap sysout
+                    MapBean.suppressCopyright = true;
+        
+                    // configure swing session
+                    // can't be in config ? getUserConfigDirectory() not static
+                    File isisConfigDirectory = new File(config.getUserConfigDirectory(), "isis-fish");
+                    isisConfigDirectory.mkdirs();
+                    File sessionFile = new File(isisConfigDirectory, "session.xml");
+                    final SwingSession session = new SwingSession(sessionFile, true);
+        
+                    // lauch first UI (welcomeUI)
+                    WelcomeUI welcome = new WelcomeUI();
+                    welcome.setTitle(_("isisfish.welcome.title", IsisConfig.getVersion()));
+                    // Set to exit on close
+                    welcome.setDefaultCloseOperation(WelcomeUI.DO_NOTHING_ON_CLOSE);
+                    welcome.addWindowListener(new WindowAdapter() {
+                        @Override
+                        public void windowClosing(WindowEvent e) {
+                            WelcomeUI ui = (WelcomeUI)e.getSource();
+                            ui.getHandler().close(ui);
                         }
-                        if (!(lastCause instanceof NumberFormatException)) {
-                            ErrorHelper.showErrorDialog(null, cause.getMessage(), cause);
+        
+                        @Override
+                        public void windowClosed(WindowEvent e) {
+                            session.save();
+                            quit();
                         }
+                    });
+                    
+                    try {
+                        InputStream imageStream = WelcomeUI.class.getResourceAsStream("/images/simulation.gif");
+                        Image image = ImageIO.read(imageStream);
+                        welcome.setIconImage(image);
                     }
+                    catch (IOException ex) {
+                        if (log.isErrorEnabled()) {
+                            log.error("Can't set frame icon", ex);
+                        }
+                    }
+        
+                    // show main isis window
+                    welcome.setLocationRelativeTo(null);
+                    session.add(welcome);
+                    
+                    // small fix to set selected tab index always to first
+                    WelcomeTabUI tabUI = (WelcomeTabUI)welcome.getWelcomePanelUI().getComponent(1);
+                    tabUI.getSimulUI().getBodyTabbedPane().setSelectedIndex(0);
+                    tabUI.getSensitivityUI().getBodyTabbedPane().setSelectedIndex(0);
+        
+                    // display frame
+                    welcome.setVisible(true);
+        
+                    // 
+                    SimulationService service = SimulationService.getService();
+                    SimulationMonitor.getInstance().reloadConfig(service);
                 }
             });
-
-            // init simulater manager
-            SimulationService.getService();
-
-            // init IsisTray
-            IsisTray.getInstance();
-
-            // OpenMap sysout
-            MapBean.suppressCopyright = true;
-
-            // configure swing session
-            // can't be in config ? getUserConfigDirectory() not static
-            File isisConfigDirectory = new File(config.getUserConfigDirectory(), "isis-fish");
-            isisConfigDirectory.mkdirs();
-            File sessionFile = new File(isisConfigDirectory, "session.xml");
-            final SwingSession session = new SwingSession(sessionFile, true);
-
-            // lauch first UI (welcomeUI)
-            WelcomeUI welcome = new WelcomeUI();
-            welcome.setTitle(_("isisfish.welcome.title", IsisConfig.getVersion()));
-            // Set to exit on close
-            welcome.setDefaultCloseOperation(WelcomeUI.DO_NOTHING_ON_CLOSE);
-            welcome.addWindowListener(new WindowAdapter() {
-                @Override
-                public void windowClosing(WindowEvent e) {
-                    WelcomeUI ui = (WelcomeUI)e.getSource();
-                    ui.getHandler().close(ui);
-                }
-
-                @Override
-                public void windowClosed(WindowEvent e) {
-                    session.save();
-                    quit();
-                }
-            });
-            
-            try {
-                InputStream imageStream = WelcomeUI.class.getResourceAsStream("/images/simulation.gif");
-                Image image = ImageIO.read(imageStream);
-                welcome.setIconImage(image);
-            }
-            catch (IOException ex) {
-                if (log.isErrorEnabled()) {
-                    log.error("Can't set frame icon", ex);
-                }
-            }
-
-            // show main isis window
-            welcome.setLocationRelativeTo(null);
-            session.add(welcome);
-            
-            // small fix to set selected tab index always to first
-            WelcomeTabUI tabUI = (WelcomeTabUI)welcome.getWelcomePanelUI().getComponent(1);
-            tabUI.getSimulUI().getBodyTabbedPane().setSelectedIndex(0);
-            tabUI.getSensitivityUI().getBodyTabbedPane().setSelectedIndex(0);
-
-            // display frame
-            welcome.setVisible(true);
         }
         else {
             if (log.isInfoEnabled()) {

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/aspect/CacheAspect.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -36,7 +36,7 @@
 import org.aspectj.lang.reflect.MethodSignature;
 
 import fr.ifremer.isisfish.simulator.SimulationContext;
-import fr.ifremer.isisfish.util.Cache;
+import fr.ifremer.isisfish.util.IsisCache;
 
 /**
  * CacheAspect aspect.
@@ -66,9 +66,9 @@
      *
      * @return trace object from context
      */
-    protected Cache getCache() {
+    protected IsisCache getCache() {
         SimulationContext context = SimulationContext.get();
-        Cache result = context.getCache();
+        IsisCache result = context.getCache();
         return result;
     }
 

Copied: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java (from rev 3892, trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java)
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java	                        (rev 0)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageInMemory.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -0,0 +1,497 @@
+/*
+ * #%L
+ * IsisFish
+ * 
+ * $Id$
+ * $HeadURL$
+ * %%
+ * Copyright (C) 2002 - 2011 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric
+ * %%
+ * 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 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package fr.ifremer.isisfish.datastore;
+
+import static org.nuiton.i18n.I18n._;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.nuiton.math.matrix.MatrixFactory;
+import org.nuiton.math.matrix.MatrixIterator;
+import org.nuiton.math.matrix.MatrixND;
+import org.nuiton.topia.TopiaContext;
+import org.nuiton.util.ArrayUtil;
+import org.nuiton.util.HashList;
+
+import fr.ifremer.isisfish.IsisFishException;
+import fr.ifremer.isisfish.entities.Population;
+import fr.ifremer.isisfish.export.Export;
+import fr.ifremer.isisfish.export.SensitivityExport;
+import fr.ifremer.isisfish.rule.Rule;
+import fr.ifremer.isisfish.simulator.SimulationContext;
+import fr.ifremer.isisfish.simulator.SimulationException;
+import fr.ifremer.isisfish.simulator.SimulationPlan;
+import fr.ifremer.isisfish.simulator.SimulationResultGetter;
+import fr.ifremer.isisfish.types.TimeStep;
+import fr.ifremer.isisfish.types.Month;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.LinkedList;
+import java.util.Map;
+
+/**
+ * Cette classe permet de conserver des résultats de simulation. Elle permet
+ * ensuite de les récupérer. Les résultats sont stockés en mémoire.
+ * 
+ * Created: 29 sept. 2004
+ *
+ * @author Benjamin Poussin <poussin@codelutin.com>
+ * @version $Revision$
+ *
+ * Mise a jour: $Date$
+ * par : $Author$
+ */
+public class ResultStorageInMemory implements SimulationResultGetter, ResultStorage {
+
+    /** to use log facility, just put in your code: log.info(\"...\"); */
+    static private Log log = LogFactory.getLog(ResultStorageInMemory.class);
+
+    final static public String MAX_TIME_STEP = "ResultStorageInMemory.maxTimeStep";
+    protected int maxTimeStep = 12; // default to 1 year
+    protected SimulationStorage simulation = null;
+
+    LinkedHashMap<TimeStep, Map<String, MatrixND>> data = new LinkedHashMap<TimeStep, Map<String, MatrixND>>() {
+        private static final long serialVersionUID = 1L;
+        @Override
+        protected boolean removeEldestEntry(Map.Entry eldest) {
+            return size() > maxTimeStep;
+        }
+    };
+
+    LinkedHashMap<TimeStep, List<Rule>> rules = new LinkedHashMap<TimeStep, List<Rule>>() {
+        private static final long serialVersionUID = 1L;
+        @Override
+        protected boolean removeEldestEntry(Map.Entry eldest) {
+            return size() > maxTimeStep;
+        }
+    };
+
+
+    /** result enabled */
+    transient protected Set<String> enabledResult = null;
+
+    /**
+     * Les ResultStorage ne doivent pas etre instancier directement, mais
+     * recuperer a partir d'un
+     * {@link fr.ifremer.isisfish.datastore.SimulationStorage#getResultStorage()}
+     * 
+     * @param simulation storage to get result
+     */
+    public ResultStorageInMemory(SimulationStorage simulation) {
+        this.simulation = simulation;
+        maxTimeStep = Integer.parseInt(simulation.getParameter().getTagValue().get(MAX_TIME_STEP));
+    }
+
+    @Override
+    public void delete() {
+        data.clear();
+    }
+
+    @Override
+    public void close() {
+        // do nothing, closed by simulation storage closing
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#isEnabled(java.lang.String)
+     */
+    @Override
+    public boolean isEnabled(String name) {
+        name = name.trim();
+        if (enabledResult == null) {
+            enabledResult = new HashSet<String>();
+
+            Collection<String> resultEnabled = simulation.getParameter()
+                    .getResultEnabled();
+            enabledResult.addAll(resultEnabled);
+
+            // test on export
+            List<String> exportNames = simulation.getParameter().getExportNames();
+            if (exportNames != null) {
+                for (String exportName : exportNames) {
+                    ExportStorage storage = ExportStorage.getExport(exportName);
+                    try {
+                        Export export = storage.getNewExportInstance();
+                        for (String resultName : export.getNecessaryResult()) {
+                            enabledResult.add(resultName);
+                        }
+                    } catch (IsisFishException eee) {
+                        if (log.isWarnEnabled()) {
+                            log.warn(_("isisfish.error.instanciate.export",
+                                            exportName), eee);
+                        }
+                    }
+                }
+            }
+
+            // test on sensitivity export
+            List<SensitivityExport> sensitivityExports = simulation
+                    .getParameter().getSensitivityExport();
+            if (sensitivityExports != null) {
+                for (SensitivityExport sensitivityExport : sensitivityExports) {
+                    for (String resultName : sensitivityExport.getNecessaryResult()) {
+                        enabledResult.add(resultName);
+                    }
+                }
+            }
+
+            // test on rules
+            List<Rule> rules = simulation.getParameter().getRules();
+            if (rules != null) {
+                for (Rule rule : rules) {
+                    for (String resultName : rule.getNecessaryResult()) {
+                        enabledResult.add(resultName);
+                    }
+                }
+            }
+
+            // test on plans
+            List<SimulationPlan> plans = simulation.getParameter().getSimulationPlans();
+            if (plans != null) {
+                for (SimulationPlan plan : plans) {
+                    for (String resultName : plan.getNecessaryResult()) {
+                        enabledResult.add(resultName);
+                    }
+                }
+            }
+            log.info("Enabled result: " + enabledResult);
+        }
+        boolean result = enabledResult.contains(name);
+        return result;
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(TimeStep step, MatrixND mat) throws IsisFishException {
+        addResult(false, step, mat.getName(), mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(TimeStep step, Population pop, MatrixND mat) throws IsisFishException {
+        addResult(false, step, mat.getName(), pop, mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(boolean force, TimeStep step, MatrixND mat) throws IsisFishException {
+        addResult(force, step, mat.getName(), mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(boolean force, TimeStep step, Population pop, MatrixND mat) throws IsisFishException {
+        addResult(force, step, mat.getName(), pop, mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, java.lang.String, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException {
+        addResult(false, step, name, pop, mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(TimeStep step, String name, MatrixND mat) throws IsisFishException {
+        addResult(false, step, name, mat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, java.lang.String, fr.ifremer.isisfish.entities.Population, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(boolean force, TimeStep step, String name, Population pop, MatrixND mat) throws IsisFishException {
+        if (force || isEnabled(name)) {
+            doAddResult(step, name + " " + pop, mat);
+        }
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addResult(boolean, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(boolean force, TimeStep step, String name, MatrixND mat) throws IsisFishException {
+        if (force || isEnabled(name)) {
+            doAddResult(step, name, mat);
+        }
+    }
+
+    protected void doAddResult(TimeStep step, String name, MatrixND mat) throws IsisFishException {
+        // si la matrice n'a pas de semantique on refuse
+        for (int i = 0; i < mat.getDimCount(); i++) {
+            // la semantique n'est pas bonne des qu'il y a un null dedans
+            if (mat.getSemantic(i).contains(null)) {
+                throw new SimulationException(
+                        "Erreur le résultat que vous souhaitez enregistrer n'a pas d'information convenable pour la dimension: "
+                                + i + " " + mat.getDimensionName(i));
+            }
+        }
+
+        // on fait une copie pour avoir reellement des resultats independant
+        // FIXME echatellier 20120829 : faire une copie optimiser
+        // suivant l'implementation du vector plutot qu'un parcourt
+        // via un iterateur de semantiques (plus couteux)
+        MatrixND newMat = mat.copy();
+        Map<String, MatrixND> mats = data.get(step);
+        if (mats == null) {
+            mats = new HashMap<String, MatrixND>();
+            data.put(step, mats);
+        }
+
+        mats.put(name, newMat);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#addActiveRule(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.rule.Rule)
+     */
+    @Override
+    public void addActiveRule(TimeStep step, Rule rule) throws IsisFishException {
+        List<Rule> list = rules.get(step);
+        if (list == null) {
+            list = new LinkedList<Rule>();
+            rules.put(step, list);
+        }
+
+        list.add(rule);
+
+//        result.setActiveRuleStep(step);
+//        result.setName(RuleStorage.getName(rule));
+//        result.setParam(RuleStorage.getParamAsString(rule));
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getResultName()
+     */
+    @Override
+    public List<String> getResultName() {
+
+        Set<String> result = new HashSet<String>();
+
+        for (Map<String, MatrixND> mats : data.values()) {
+            result.addAll(mats.keySet());
+        }
+
+        return new ArrayList<String>(result);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.types.TimeStep, fr.ifremer.isisfish.entities.Population, java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(TimeStep step, Population pop, String name) {
+        String newName = name + " " + pop;
+        return getMatrix(step, newName);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.types.TimeStep, java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(TimeStep step, String name) {
+        MatrixND result = null;
+        Map<String, MatrixND> mats = data.get(step);
+        if (mats != null) {
+            result = mats.get(name);
+        }
+        return result;
+    }
+
+    @Override
+    public MatrixND getMatrix(TimeStep step, String name, TopiaContext tx) {
+        return getMatrix(step, name);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.entities.Population, java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(Population pop, String name) {
+        String newName = name + " " + pop;
+        return getMatrix(newName);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(fr.ifremer.isisfish.entities.Population, java.lang.String, org.nuiton.topia.TopiaContext)
+     */
+    @Override
+    public MatrixND getMatrix(Population pop, String name, TopiaContext tx) {
+        String newName = name + " " + pop;
+        return getMatrix(newName, tx);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(String name) {
+        MatrixND result = null;
+        
+        List<TimeStep> steps = new ArrayList<TimeStep>();
+        Map<TimeStep, MatrixND> mats = new LinkedHashMap<TimeStep, MatrixND>();
+        MatrixND matExample = null;
+        for (Map.Entry<TimeStep, Map<String, MatrixND>> e : data.entrySet()) {
+            TimeStep ts = e.getKey();
+            MatrixND mat = e.getValue().get(name);
+            if (mat != null) {
+                steps.add(ts);
+                mats.put(ts, mat);
+                matExample = mat;
+            }
+        }
+
+        if (mats.size() > 0) {
+            // recuperation des noms des dimensions
+            String[] dimNames = new String[1 + matExample.getDimCount()];
+            dimNames[0] = _("isisfish.common.date");
+            for (int i = 1; i < dimNames.length; i++) {
+                dimNames[i] = matExample.getDimensionName(i - 1);
+            }
+
+            // creation de la semantique pour la matrice resultat. +1 pour les dates
+            List[] sem = new List[1 + matExample.getDimCount()];
+            sem[0] = steps;
+
+            for (int i = 1; i < sem.length; i++) {
+                sem[i] = new HashList();
+            }
+
+            for (MatrixND mattmp : mats.values()) {
+                if (log.isTraceEnabled()) {
+                    log.trace("Ajout de la semantics: "
+                            + Arrays.asList(mattmp.getSemantics()));
+                }
+
+                for (int s = 0; s < mattmp.getDimCount(); s++) {
+                    sem[s + 1].addAll(mattmp.getSemantic(s));
+                }
+            }
+
+            if (log.isTraceEnabled()) {
+                log.trace("La semantique final est: " + Arrays.asList(sem));
+            }
+
+            // creation de la matrice resultat
+            result = MatrixFactory.getInstance().create(name, sem, dimNames);
+
+            // recuperation du resultat pour chaque date de la simulation, de Date(0) à lastDate
+            for (Map.Entry<TimeStep, MatrixND> e : mats.entrySet()) {
+                TimeStep d = e.getKey();
+                MatrixND mat = e.getValue();
+                // on recupere dans la matrice resultat l'endroit on il faut
+                // mettre la matrice
+                MatrixND submat = result.getSubMatrix(0, d, 1);
+                // on met les valeur de mat dans la sous matrice extraite
+                for (MatrixIterator mi = mat.iterator(); mi.next();) {
+                    submat.setValue(
+                            ArrayUtil.concat(new Object[] { d },
+                                    mi.getSemanticsCoordinates()), mi.getValue());
+                }
+            }
+        }
+
+        return result;
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getMatrix(java.lang.String, org.nuiton.topia.TopiaContext)
+     */
+    @Override
+    public MatrixND getMatrix(String name, TopiaContext tx) {
+        return getMatrix(name);
+    }
+
+    /* (non-Javadoc)
+     * @see fr.ifremer.isisfish.datastore.ResultStorage#getLastStep()
+     */
+    @Override
+    public TimeStep getLastStep() {
+        int monthNumber = simulation.getParameter().getNumberOfYear()
+                * Month.NUMBER_OF_MONTH;
+        TimeStep result = new TimeStep(monthNumber - 1); // -1 because date begin at 0
+        return result;
+    }
+
+    /*
+     * @see fr.ifremer.isisfish.simulator.SimulationResultListener#addResult(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String, org.nuiton.math.matrix.MatrixND)
+     */
+    @Override
+    public void addResult(SimulationContext context, TimeStep step, String name,
+            MatrixND mat) throws IsisFishException {
+        doAddResult(step, name, mat);
+    }
+
+    /*
+     * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, fr.ifremer.isisfish.types.TimeStep, java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(SimulationContext context, TimeStep step, String name) {
+        MatrixND result = getMatrix(step, name);
+        return result;
+    }
+
+    /*
+     * @see fr.ifremer.isisfish.simulator.SimulationResultGetter#getMatrix(fr.ifremer.isisfish.simulator.SimulationContext, java.lang.String)
+     */
+    @Override
+    public MatrixND getMatrix(SimulationContext context, String name) {
+        MatrixND result = getMatrix(name);
+        return result;
+    }
+
+    /*
+     * @see fr.ifremer.isisfish.simulator.SimulationListener#afterSimulation(fr.ifremer.isisfish.simulator.SimulationContext)
+     */
+    @Override
+    public void afterSimulation(SimulationContext context) {
+    }
+
+    /*
+     * @see fr.ifremer.isisfish.simulator.SimulationListener#beforeSimulation(fr.ifremer.isisfish.simulator.SimulationContext)
+     */
+    @Override
+    public void beforeSimulation(SimulationContext context) {
+    }
+
+}

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -476,10 +476,17 @@
             if (simuVersion.before(version4200)) {
                 resultStorage = new ResultDatabaseStorage(this);
             } else {
-                try {
-                    resultStorage = new ResultMappedStorage(this);
-                } catch (IOException ex) {
-                    throw new StorageException("Can't get storage", ex);
+                // if user ask for ResultStorageInMemory, used it
+                String maxTimeStep = param.getTagValue().get(ResultStorageInMemory.MAX_TIME_STEP);
+                if (maxTimeStep != null) {
+                    // use in memory with max time step
+                    resultStorage = new ResultStorageInMemory(this);
+                } else {
+                    try {
+                        resultStorage = new ResultMappedStorage(this);
+                    } catch (IOException ex) {
+                        throw new StorageException("Can't get storage", ex);
+                    }
                 }
             }
         }

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/equation/PopulationGrowth.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/equation/PopulationGrowth.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/equation/PopulationGrowth.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -43,7 +43,7 @@
 public interface PopulationGrowth {
     
     /**
-     * Compute groth equation.
+     * Compute growth equation.
      * 
      * @param context simulation context
      * @param age l'age du groupe en mois

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -40,7 +40,7 @@
 import fr.ifremer.isisfish.datastore.SimulationStorage;
 import fr.ifremer.isisfish.simulator.sensitivity.SensitivityUtils;
 import fr.ifremer.isisfish.types.TimeStep;
-import fr.ifremer.isisfish.util.Cache;
+import fr.ifremer.isisfish.util.IsisCache;
 import fr.ifremer.isisfish.util.Trace;
 
 /**
@@ -78,7 +78,7 @@
     /** l'objet trace qui conserve les donnees statistiques des appels de methodes */
     protected Trace trace;
     /** cache used by aspect for this simulation */
-    protected Cache cache;
+    protected IsisCache cache;
 
     /** TopiaContext must be used by rule action to modify data */
     protected TopiaContext db = null;
@@ -208,10 +208,11 @@
         return trace;
     }
 
-    public Cache getCache() {
+    public IsisCache getCache() {
         if (cache == null) {
-            cache = new Cache();
-        }return cache;
+            cache = new IsisCache();
+        }
+        return cache;
     }
 
     /**

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -201,9 +201,10 @@
         // fait un appel au moniteur
         // pour reprendre le monitoring des simulation en cours
         // TODO check this, don't restart monitoring on non ui launch
-        if (IsisFish.config.isLaunchUI()) {
-            SimulationMonitor.getInstance().reloadConfig(this);
-        }
+        // moved to main()
+        //if (IsisFish.config.isLaunchUI()) {
+        //    SimulationMonitor.getInstance().reloadConfig(this);
+        //}
     }
 
     /**

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationServiceTableModel.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -103,7 +103,7 @@
         }
         controlListener = new ControlListener(this);
         simulationService.addSimulationServiceListener(jobListener);
-        jobListener.setData();
+        //jobListener.setData();
     }
 
     public void addJob(SimulationJob job) {
@@ -330,12 +330,12 @@
         }
 
         public void setData() {
-            model.setJobs(new ArrayList<SimulationJob>(simulationService
-                    .getJobs()));
-            for (SimulationJob job : model.getJobs()) {
+            ArrayList<SimulationJob> jobs = new ArrayList<SimulationJob>(simulationService.getJobs());
+            for (SimulationJob job : jobs) {
                 job.getItem().getControl().addPropertyChangeListener(
                         controlListener);
             }
+            model.setJobs(jobs);
         }
 
         public void simulationStart(SimulationService simService,

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesEditorUI.jaxx	2014-03-19 09:51:00 UTC (rev 3893)
@@ -192,7 +192,9 @@
                 <cell columns='3' fill='both' weightx='1.0' weighty='0.5'>
                     <org.nuiton.math.matrix.gui.MatrixPanelEditor id='fieldPopulationMappingZoneReproZoneRecru'
                         constructorParams='false' enabled='{isActive()}'
-                        onMatrixChanged="populationMappingZoneReproZoneRecruMatrixChanged(event)" />
+                        onMatrixChanged="populationMappingZoneReproZoneRecruMatrixChanged(event)"
+                        decorator='boxed'
+                        _sensitivityBean='{fr.ifremer.isisfish.entities.Population.class}' _sensitivityMethod='"MappingZoneReproZoneRecru"' />
                 </cell>
             </row>
         </Table>

Modified: branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/ui/input/PopulationZonesUI.jaxx	2014-03-19 09:51:00 UTC (rev 3893)
@@ -43,6 +43,12 @@
 
     getSaveVerifier().addCurrentPanel(popZones);
 }*/
+
+@Override
+public void setLayer(boolean active) {
+    super.setLayer(active);
+    popZones.setLayer(active);
+}
     ]]>
     </script>
     <JPanel id='body'>
@@ -50,8 +56,7 @@
             <row>
                 <cell columns="2" fill='both' weightx='1.0' weighty='1'>
                     <PopulationZonesEditorUI id='popZones' constructorParams='this'
-                        bean='{getBean()}' active='{isActive()}' decorator='boxed'
-                        _sensitivityBean='{Population.class}' _sensitivityMethod='"MappingZoneReproZoneRecru"'/>
+                        bean='{getBean()}' active='{isActive()}'/>
                 </cell>
             </row>
             <row>

Deleted: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/Cache.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -1,288 +0,0 @@
-/*
- * #%L
- * IsisFish
- * 
- * $Id$
- * $HeadURL$
- * %%
- * Copyright (C) 2006 - 2013 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin, Chatellier Eric
- * %%
- * 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 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 General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public 
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-3.0.html>.
- * #L%
- */
-
-package fr.ifremer.isisfish.util;
-
-import java.lang.reflect.Method;
-import java.util.Map;
-
-import org.apache.commons.collections4.map.AbstractReferenceMap.ReferenceStrength;
-import org.apache.commons.collections4.map.ReferenceMap;
-import org.aspectj.lang.ProceedingJoinPoint;
-import org.nuiton.topia.persistence.TopiaEntity;
-
-import fr.ifremer.isisfish.simulator.SimulationContext;
-import fr.ifremer.isisfish.types.TimeStep;
-
-/**
- * Cache utilise pour mettre les resultats de methode durant la simulation
- * pour minimiser les appels
- * 
- * Created: 25 août 06 22:42:47
- *
- * @author poussin
- * @version $Revision$
- *
- * Last update: $Date$
- * by : $Author$
- */
-public class Cache {
-
-    // la longueur du package pour minimiser la longueur des topiaId
-    static final private int entityPackageLenght = "fr.ifremer.isisfish.entities.".length();
-    // la valeur NULL a utilise a la place de null pour les timeStep
-    static final private Object NULL = new Object();
-
-//    static private List<CacheAspect> instances = new ArrayList<CacheAspect>();
-    
-    protected long totalCall = 0;
-    protected long cacheUsed = 0;
-
-    /**
-     * map<TimeStep, Map<Key, Value>>
-     * TimeStep peut etre null via l'objet NULL
-     * Key est la cle calcule par computeKey
-     * Value est la valeur du cache
-     *
-     * TimeStep est en WEAK pour que des que l'on passe au pas de temps suivant
-     * ils soit efface de la memoire si plus personne n'a de reference sur
-     * ce pas de temps. L'autre moyen est de force l'effacement via clear(TimeStep)
-     *
-     * Value est en SOFT reference pour que les valeurs soit effacee du cache
-     * lorsqu'il n'y a plus de place memoire
-     */
-    protected Map cache = new ReferenceMap(ReferenceStrength.WEAK, ReferenceStrength.HARD);
-//    protected Map cache = new AdaptaptativeCache(1000, 95);
-    
-    public Cache() {
-    }
-
-    /**
-     * Return trace object from context.
-     *
-     * @return trace object from context
-     */
-    protected Trace getTrace() {
-        SimulationContext context = SimulationContext.get();
-        Trace result = context.getTrace();
-        return result;
-    }
-
-    /**
-     * Recupere pour un pas de temps donnes une valeur calcule pour une cle
-     * @param step le pas de temps pour lequel on souhaite ajouter (ou null)
-     * @param key la cle de storage
-     * @param defaultValue la valeur par defaut a retourner si elle n'est pas en cache
-     * si defaultValue est une JoinPoint alors un proceed est appele dessus et le
-     * resultat de l'appel est utiliser comme valeur par defaut
-     * @return la valeur dans le cache ou defaultValue
-     */
-    public Object get(Method method, Object[] args, Object defaultValue) throws Throwable {
-        totalCall++;
-
-        Object result = null;
-        if (method.getAnnotation(Nocache.class) != null ||
-                method.getDeclaringClass().getAnnotation(Nocache.class) != null) {
-            result = realCall(defaultValue);
-        } else {
-            // compute key and keep TimeStep objet
-            StringBuilder sbKey = new StringBuilder();
-            // le pas de temps trouve dans les arguments
-            TimeStep step = computeKey(sbKey, method, args);
-
-            // on recupere le intern de la String car normalement en cache on
-            // retrouve souvent les memes chaines comme cle (sinon le cache
-            // servirait a rien :D)
-            Object key = sbKey.toString().intern();
-            result = get(step, key);
-            if (result == null) {
-
-                // computation increment (/ by 0)
-                // FIXME need to be called, but fail with empty stack
-                //getTrace().traceAfterComputation(method);
-
-                result = realCall(defaultValue);
-                if (result != null) { // util pour les methodes retournant void, ne fonctionne pas si on met AND !execute(void *(..)) dans l'aspect. En fait fonction seulement si utilisé avec les traces :(
-                    put(step, key, result);
-                }
-            } else {
-                cacheUsed++;
-            }
-        }
-        return result;
-    }
-
-    protected TimeStep computeKey(StringBuilder sbKey, Method method, Object[] args) {
-        TimeStep result = null;
-        sbKey.append(method.getDeclaringClass().getSimpleName());
-        sbKey.append(".");
-        sbKey.append(method.getName());
-        for (Object o : args) {
-            sbKey.append(";");
-            if (o == null) {
-                sbKey.append("null");
-            } else if (o instanceof Number || o instanceof String) {
-                sbKey.append(o.toString());
-            } else if (o instanceof TimeStep) {
-                result = (TimeStep)o;
-                sbKey.append(((TimeStep)o).getStep());
-            } else if (o instanceof TopiaEntity) {
-                sbKey.append( ((TopiaEntity)o).getTopiaId().substring(entityPackageLenght));
-            } else {
-                // on minimise en prenant que le nom de la classe (pas le package)
-                sbKey.append(o.getClass().getSimpleName());
-                sbKey.append('@');
-                // et en lui ajoutant son adresse memoire en Hexa
-                sbKey.append(Integer.toHexString(System.identityHashCode(o)));
-            }
-        }
-        return result;
-    }
-
-    protected Map getCacheTimeStep(TimeStep step) {
-        Object key = step;
-        if (step == null)  {
-            key = NULL;
-        }
-        Map result = (Map)cache.get(key);
-        if (result == null) {
-            result = new ReferenceMap(ReferenceStrength.HARD, ReferenceStrength.SOFT);
-            cache.put(key, result);
-        }
-        return result;
-    }
-
-    protected Object get(TimeStep step, Object key) {
-        Object result = null;
-        Map cacheTimeStep = getCacheTimeStep(step);
-        if (cacheTimeStep != null) {
-            result = cacheTimeStep.get(key);
-        }
-        return result;
-    }
-
-    protected void put(TimeStep step, Object key, Object value) {
-        getCacheTimeStep(step).put(key, value);
-    }
-
-    /**
-     * On fait l'appel reel dans une autre methode pour pouvoir le savoir
-     * dans les traces
-     * 
-     * @param jp
-     * @return ?
-     * @throws Throwable
-     */
-    protected Object realCall(Object defaultValue) throws Throwable {
-        Object result = defaultValue;
-        if (defaultValue instanceof ProceedingJoinPoint) {
-            result = ((ProceedingJoinPoint)defaultValue).proceed();
-        }
-        return result;
-    }
-
-    /**
-     * remove all values in cache
-     */
-    public void clear() {
-        cache.clear();
-    }
-
-    /**
-     * remove all values in cache for the specied TimeStep
-     */
-    public void clear(TimeStep step) {
-        Object key = step;
-        if (key == null) {
-            key = NULL;
-        }
-        cache.remove(key);
-    }
-    
-    /**
-     * @return Returns the cacheUsed.
-     */
-    public long getCacheUsed() {
-        long result = cacheUsed;
-        return result;
-    }
-    
-    /**
-     * @return Returns the totalCall.
-     */
-    public long getTotalCall() {
-        long result = totalCall;
-        return result;
-    }
-    
-    /**
-     * Affiche les statistiques
-     *
-     */
-    public String printStatistiqueAndClear() {
-        StringBuilder result = new StringBuilder();
-        result.append("--- Cache Statistiques ---\n");
-        result.append("Total call: ").append(totalCall).append("\n");
-        result.append("Cache used: ").append(cacheUsed).append("\n");
-        long percent = 0;
-        if (totalCall != 0) {
-            percent = 100*cacheUsed/totalCall;
-        }
-        result.append("Cache usage: ").append(percent).append("%\n");
-        result.append("--------------------\n");
-        cache.clear();
-
-        System.out.println(result.toString());
-        return result.toString();
-    }
-
-    // EN COURS D'ECRITURE MAIS JAMAIS FINI :(
-    // l'idee est de prendre la place memoire qu'il y a, mais s'il n'y en
-    // a plus on commence par enlever les objets les plus vieux
-//    class AdaptaptativeCache extends LinkedHashMap<String, Object> {
-//        protected int maxMemory = 95;
-//        /**
-//         *
-//         * @param capacity initial capacity
-//         * @param maxMemory maximum memory used (0-100)
-//         */
-//        public AdaptaptativeCache(int capacity, int maxMemory) {
-//            super(capacity, 0.75f, true);
-//            this.maxMemory = maxMemory;
-//        }
-//
-//        /* (non-Javadoc)
-//         * @see java.util.LinkedHashMap#removeEldestEntry(java.util.Map.Entry)
-//         */
-//        @Override
-//        protected boolean removeEldestEntry(Entry<String, Object> eldest) {
-//            double free = 100.0 * Runtime.getRuntime().freeMemory() / Runtime.getRuntime().maxMemory() ;
-//            boolean result = 100 - free > maxMemory;
-//            return result;
-//        }
-//    }
-}
-
-

Copied: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCache.java (from rev 3892, trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java)
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCache.java	                        (rev 0)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCache.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -0,0 +1,268 @@
+/*
+ * #%L
+ * IsisFish
+ * 
+ * $Id$
+ * $HeadURL$
+ * %%
+ * Copyright (C) 2006 - 2010 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin
+ * %%
+ * 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 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+package fr.ifremer.isisfish.util;
+
+import java.lang.reflect.Method;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.aspectj.lang.ProceedingJoinPoint;
+import org.nuiton.topia.persistence.TopiaEntity;
+
+import fr.ifremer.isisfish.simulator.SimulationContext;
+import fr.ifremer.isisfish.types.TimeStep;
+
+/**
+ * IsisCacheOnReferenceMap utilise pour mettre les resultats de methode durant
+ * la simulation pour minimiser les appels
+ * <p>
+ * Created: 25 août 06 22:42:47
+ * <p>
+ * @author poussin
+ * @version $Revision$
+ <p>
+ Last update: $Date$ by :
+ $Author$
+ */
+public class IsisCache {
+
+    /**
+     * to use log facility, just put in your code: log.info(\"...\");
+     */
+    static private Log log = LogFactory.getLog(IsisCache.class);
+
+    static public IsisCacheBackend.Factory defaultFactory
+            = IsisCacheBackendOnGuava.factory;
+
+    // la longueur du package pour minimiser la longueur des topiaId
+    static final private int entityPackageLenght = "fr.ifremer.isisfish.entities.".length();
+    // la valeur NULL a utilise a la place de null pour les timeStep
+    static final private Object NULL = new Object();
+
+    protected long totalCall = 0;
+    protected long cacheUsed = 0;
+
+    protected IsisCacheBackend cacheBackend;
+
+    public IsisCache() {
+        this(defaultFactory.createNew());
+    }
+
+    public IsisCache(IsisCacheBackend cacheBackend) {
+        this.cacheBackend = cacheBackend;
+    }
+
+    /**
+     * Return trace object from context.
+     * <p>
+     * @return trace object from context
+     */
+    protected Trace getTrace() {
+        SimulationContext context = SimulationContext.get();
+        Trace result = context.getTrace();
+        return result;
+    }
+
+    /**
+     * Recupere pour un pas de temps donnes une valeur calcule pour une cle
+     * <p>
+     * @param step         le pas de temps pour lequel on souhaite ajouter (ou
+     *                     null)
+     * @param key          la cle de storage
+     * @param defaultValue la valeur par defaut a retourner si elle n'est pas en
+     *                     cache si defaultValue est une JoinPoint alors un
+     *                     proceed est appele dessus et le resultat de l'appel
+     *                     est utiliser comme valeur par defaut
+     * @return la valeur dans le cache ou defaultValue
+     */
+    public Object get(Method method, Object[] args, Object defaultValue) throws Throwable {
+        totalCall++;
+
+        Object result = null;
+        if (method.getAnnotation(Nocache.class) != null
+                || method.getDeclaringClass().getAnnotation(Nocache.class) != null) {
+            result = realCall(defaultValue);
+        } else {
+            // compute key and keep TimeStep objet
+            StringBuilder sbKey = new StringBuilder();
+            // le pas de temps trouve dans les arguments
+            TimeStep step = computeKey(sbKey, method, args);
+
+            // on recupere le intern de la String car normalement en cache on
+            // retrouve souvent les memes chaines comme cle (sinon le cache
+            // servirait a rien :D)
+            String key = sbKey.toString().intern();
+            result = get(step, key);
+            if (result == null) {
+
+                // computation increment (/ by 0)
+                // FIXME need to be called, but fail with empty stack
+                //getTrace().traceAfterComputation(method);
+                result = realCall(defaultValue);
+                if (result != null) { // util pour les methodes retournant void, ne fonctionne pas si on met AND !execute(void *(..)) dans l'aspect. En fait fonction seulement si utilisé avec les traces :(
+                    put(step, key, result);
+                }
+            } else {
+                cacheUsed++;
+            }
+        }
+        return result;
+    }
+
+    protected TimeStep computeKey(StringBuilder sbKey, Method method, Object[] args) {
+        TimeStep result = null;
+        sbKey.append(method.getDeclaringClass().getSimpleName());
+        sbKey.append(".");
+        sbKey.append(method.getName());
+        for (Object o : args) {
+            sbKey.append(";");
+            if (o == null) {
+                sbKey.append("null");
+            } else if (o instanceof Number || o instanceof String) {
+                sbKey.append(o.toString());
+            } else if (o instanceof TimeStep) {
+                result = (TimeStep) o;
+                sbKey.append(((TimeStep) o).getStep());
+            } else if (o instanceof TopiaEntity) {
+                sbKey.append(((TopiaEntity) o).getTopiaId().substring(entityPackageLenght));
+            } else {
+                // on minimise en prenant que le nom de la classe (pas le package)
+                sbKey.append(o.getClass().getSimpleName());
+                sbKey.append('@');
+                // et en lui ajoutant son adresse memoire en Hexa
+                sbKey.append(Integer.toHexString(System.identityHashCode(o)));
+            }
+        }
+        return result;
+    }
+
+    protected Object get(TimeStep step, String key) {
+        Object result = cacheBackend.get(step, key);
+        return result;
+    }
+
+    protected void put(TimeStep step, String key, Object value) {
+        cacheBackend.put(step, key, value);
+    }
+
+    /**
+     * On fait l'appel reel dans une autre methode pour pouvoir le savoir dans
+     * les traces
+     * <p>
+     * @param jp
+     * @return ?
+     * @throws Throwable
+     */
+    protected Object realCall(Object defaultValue) throws Throwable {
+        Object result = defaultValue;
+        if (defaultValue instanceof ProceedingJoinPoint) {
+            result = ((ProceedingJoinPoint)defaultValue).proceed();
+        }
+        return result;
+    }
+
+    /**
+     * remove all values in cache
+     */
+    public void clear() {
+        cacheBackend.clear();
+    }
+
+    /**
+     * remove all values in cache for the specied TimeStep
+     */
+    public void clear(TimeStep step) {
+        Object key = step;
+        if (key == null) {
+            key = NULL;
+        }
+        cacheBackend.removeStep(key);
+    }
+
+    /**
+     * @return Returns the cacheUsed.
+     */
+    public long getCacheUsed() {
+        long result = cacheUsed;
+        return result;
+    }
+
+    /**
+     * @return Returns the totalCall.
+     */
+    public long getTotalCall() {
+        long result = totalCall;
+        return result;
+    }
+
+    /**
+     * Affiche les statistiques
+     * <p>
+     */
+    public String printStatistiqueAndClear() {
+        cacheBackend.clear();
+
+        StringBuilder result = new StringBuilder();
+        result.append("--- Cache Statistiques ---\n");
+        result.append("Total call: ").append(totalCall).append("\n");
+        result.append("Cache used: ").append(cacheUsed).append("\n");
+        long percent = 0;
+        if (totalCall != 0) {
+            percent = 100 * cacheUsed / totalCall;
+        }
+        result.append("Cache usage: ").append(percent).append("%\n");
+        result.append(cacheBackend.getStat());
+        result.append("--------------------\n");
+
+        System.out.println(result.toString());
+        return result.toString();
+    }
+
+    // EN COURS D'ECRITURE MAIS JAMAIS FINI :(
+    // l'idee est de prendre la place memoire qu'il y a, mais s'il n'y en
+    // a plus on commence par enlever les objets les plus vieux
+//    class AdaptaptativeCache extends LinkedHashMap<String, Object> {
+//        protected int maxMemory = 95;
+//        /**
+//         *
+//         * @param capacity initial capacity
+//         * @param maxMemory maximum memory used (0-100)
+//         */
+//        public AdaptaptativeCache(int capacity, int maxMemory) {
+//            super(capacity, 0.75f, true);
+//            this.maxMemory = maxMemory;
+//        }
+//
+//        /* (non-Javadoc)
+//         * @see java.util.LinkedHashMap#removeEldestEntry(java.util.Map.Entry)
+//         */
+//        @Override
+//        protected boolean removeEldestEntry(Entry<String, Object> eldest) {
+//            double free = 100.0 * Runtime.getRuntime().freeMemory() / Runtime.getRuntime().maxMemory() ;
+//            boolean result = 100 - free > maxMemory;
+//            return result;
+//        }
+//    }
+}

Copied: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java (from rev 3892, trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java)
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java	                        (rev 0)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackend.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -0,0 +1,58 @@
+/*
+ * #%L
+ * IsisFish
+ * 
+ * $Id$
+ * $HeadURL$
+ * %%
+ * Copyright (C) 2013 Ifremer, Code Lutin, Benjamin Poussin
+ * %%
+ * 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 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package fr.ifremer.isisfish.util;
+
+import fr.ifremer.isisfish.types.TimeStep;
+
+/**
+ *
+ * @author poussin
+ * @version $Revision$
+ *
+ * Last update: $Date$
+ * by : $Author$
+ */
+public interface IsisCacheBackend {
+
+    Object get(TimeStep step, String key) ;
+
+    void put(TimeStep step, String key, Object value);
+
+    void clear() ;
+
+    void removeStep(Object key);
+
+    /**
+     * get specific backend cache statistic
+     * @return backend specific string cache stat representation
+     */
+    String getStat();
+
+    static public interface Factory {
+        IsisCacheBackend createNew();
+    }
+
+}

Copied: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java (from rev 3892, trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java)
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java	                        (rev 0)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -0,0 +1,310 @@
+/*
+ * #%L
+ * IsisFish
+ * 
+ * $Id$
+ * $HeadURL$
+ * %%
+ * Copyright (C) 2013 Ifremer, Code Lutin, Benjamin Poussin
+ * %%
+ * 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 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+package fr.ifremer.isisfish.util;
+
+import com.google.common.cache.Cache;
+import com.google.common.cache.CacheBuilder;
+import com.google.common.cache.Weigher;
+import fr.ifremer.isisfish.types.TimeStep;
+import java.util.Collection;
+import org.apache.commons.lang3.ClassUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.nuiton.math.matrix.MatrixND;
+import org.nuiton.util.StringUtil;
+
+/**
+ * Cache qui reserve de la place pour l'equivalent de N pas de temps dans le cache.
+ * 
+ * Une premiere instanciation du cache est faite. Puis apres le premier pas
+ * de temps on regarde la taille des objets ayant ete ajoutes au cache pour
+ * recalculer la nouvelle taille pour permettre de stocker N pas de temps.
+ *
+ * @author poussin
+ * @version $Revision$
+
+ Last update: $Date$
+ by : $Author$
+ */
+public class IsisCacheBackendOnGuava implements IsisCacheBackend {
+
+    /** to use log facility, just put in your code: log.info(\"...\"); */
+    static private Log log = LogFactory.getLog(IsisCacheBackendOnGuava.class);
+
+    final static public int POINTER_SIZE = 8;
+    final static public int DOUBLE_SIZE = 8;
+    final static public int CHAR_SIZE = 2;
+
+    /** number of time steps to cache by interpolating from the first step*/
+    // perhaps allow the configuration
+    static public int CACHE_STEP = 3;
+
+    static public class IsisCacheBackendOnGuavaFactory implements IsisCacheBackend.Factory {
+        @Override
+        public IsisCacheBackend createNew() {
+            return new IsisCacheBackendOnGuava();
+        }
+    }
+
+    static public Factory factory = new IsisCacheBackendOnGuavaFactory();
+
+    static public class IsisWeigher implements Weigher<String, Object> {
+
+        protected IsisCacheBackendOnGuava backend;
+        public IsisWeigher(IsisCacheBackendOnGuava backend) {
+            this.backend = backend;
+        }
+
+        @Override
+        public int weigh(String key, Object value) {
+            int result = key.length() * CHAR_SIZE;
+            if (value instanceof MatrixND) {
+                // MatrixND
+                // on prend le nombre de case de la matrice pour sa taille
+                // on ne tient pas compte des dimensions qui sont des objets
+                // utilises ailleurs
+                int[] dim = ((MatrixND)value).getDim();
+                int size = 1;
+                for (int i=0; i<dim.length; i++) {
+                    size *= dim[i];
+                }
+                result += size * DOUBLE_SIZE; // size is wrong, because depend on matrix type (float or double)
+            } else if (value instanceof Collection) {
+                // List<Zone|Pop|Str|Metier|Cell>
+                // on prend la taille de la collection, car la donnees
+                // elle meme qu'elle soit dans le backend ou non est
+                // certainement utilisee ailleur, donc seul la taille
+                // des pointeurs dans la collection est prise ici
+                result += ((Collection)value).size() * POINTER_SIZE;
+            } else if (value instanceof Number) {
+                // int| double
+                // seulement une valeur, on ajoute 1
+                result += 1 * DOUBLE_SIZE;
+            } else {
+                // a priori, il n'y a pas d'autre type de donnee
+                if (value != null) {
+                    log.info("Cache can't compute value size of " + ClassUtils.getPackageCanonicalName(value, "null"));
+                }
+            }
+
+            backend.addStat(result);
+            
+            result = Math.max(1024, result); // min to 1ko
+            return result;
+        }
+    }
+
+    protected Cache<String, Object> cache;
+    protected IsisWeigher isisWeigher;
+    protected long maxMemory;
+    protected long maxCache;
+    protected long sizeCache;
+
+    /** the last step use to put value in cache */
+    protected TimeStep lastStep = null;
+    /** if true size of cache has been recomputed */
+    protected boolean adjusted = false;
+
+    /** le total en octet mis en cache au precedent pas de temps*/
+    protected long totalLastStepCached = 0;
+
+    // STATISTIQUE PAR ENTREE DANS LE CACHE
+    /** le total en d'element mis en cache */
+    protected long numberCached = 0;
+    /** le total en octet mis en cache */
+    protected long totalCached = 0;
+    /** la plus petite donnee mis en cache */
+    protected long smallestCached = Long.MAX_VALUE;
+    /** la plus grosse donnee mis en cache */
+    protected long biggestCached = 0;
+
+    // for variance
+    double delta = 0;
+    double mean = 0;
+    double M2 = 0;
+
+    // STATISTIQUE PAR PAS DE TEMPS
+    /** le total en d'element mis en cache */
+    protected long numberStepCached = 0;
+    /** le total en octet mis en cache */
+    protected long totalStepCached = 0;
+    /** la plus petite donnee mis en cache */
+    protected long smallestStepCached = Long.MAX_VALUE;
+    /** la plus grosse donnee mis en cache */
+    protected long biggestStepCached = 0;
+
+    // for variance
+    double stepDelta = 0;
+    double stepMean = 0;
+    double stepM2 = 0;
+
+
+
+    public IsisCacheBackendOnGuava() {
+        isisWeigher = new IsisWeigher(this);
+
+        maxMemory = Runtime.getRuntime().maxMemory();
+        maxCache = maxMemory - 500*1024*1024; // isis need about 500M
+        maxCache = Math.max(maxCache, 200*1024*1024); // to do simulation we need 200M cache
+
+        // create first cache, this cache is juste for one step
+        adjustedCache(maxCache);
+    }
+
+    public void addStat(long value) {
+        numberCached++;
+        totalCached = totalCached + value;
+
+        // compute variance
+        delta = value - mean;
+        mean = mean + delta/numberCached;
+        M2 = M2 + delta * (value - mean);
+
+        biggestCached = Math.max(biggestCached, value);
+        smallestCached = Math.min(smallestCached, value);
+    }
+
+    public void addStepStat(long value) {
+        numberStepCached++;
+        totalStepCached = totalStepCached + value;
+
+        // compute variance
+        stepDelta = value - stepMean;
+        stepMean = stepMean + stepDelta/numberStepCached;
+        stepM2 = stepM2 + stepDelta * (value - stepMean);
+
+        biggestStepCached = Math.max(biggestStepCached, value);
+        smallestStepCached = Math.min(smallestStepCached, value);
+    }
+
+    @Override
+    public void clear() {
+        cache.invalidateAll();
+        // clear is assimilate to step change (last step end)
+        // useful to finalize variance computation for last step
+        changeStep();
+    }
+
+    @Override
+    public void removeStep(Object o) {
+    }
+
+    /**
+     * resizes the cache if amount is not greater than autorized maxCache
+     * @param amount new size of cache in byte
+     */
+    public void adjustedCache(long amount){
+        if (amount == 0) {
+            log.info("Cache size not ajusted because 0 is not acceptable amount");
+        } else {
+            // on estime le nombre d'entree necessaire pour ce volume de donnees
+            long bytePerStep = totalCached / Math.max(1, numberStepCached);
+            long entriesPerStep = numberCached / Math.max(1, numberStepCached);
+
+            long initialCapacity = amount * entriesPerStep / Math.max(1, bytePerStep);
+            long stepEquivalent = initialCapacity / Math.max(1, entriesPerStep);
+
+            // use amount as new size for cache
+            // if this new size is less than maxCache, use it
+            // to keep more memory for JVM
+            sizeCache = Math.min(this.maxCache, amount);
+        
+            CacheBuilder builder = CacheBuilder.newBuilder();
+            builder.maximumWeight(sizeCache);
+            builder.weigher(isisWeigher);
+            if (initialCapacity > 0) {
+                builder.initialCapacity((int)initialCapacity);
+            }
+            cache = builder.build();
+
+            log.info(String.format("Cache size ajusted to %s (equivalent to %s step need)",
+                    StringUtil.convertMemory(sizeCache), stepEquivalent));
+        }
+    }
+
+    /**
+     * Previent le cache, qu'on change de TimeStep et qu'il peut faire
+     * du travail s'il en a besoin.
+     *
+     * - calcul de statistique
+     * - ajustement de la taille du cache
+     */
+    public void changeStep() {
+        // on est passe au pas de temps suivant
+        long stepAmount = totalCached - totalLastStepCached;
+        totalLastStepCached = totalCached;
+        addStepStat(stepAmount);
+
+        // after first step, use information to resize cache
+        if (!adjusted) {
+            adjustedCache(stepAmount * CACHE_STEP); // keep place for 3 step
+            adjusted = true;
+        }
+    }
+
+    @Override
+    public Object get(TimeStep step, String key) {
+        Object result = cache.getIfPresent(key);
+        return result;
+    }
+
+    @Override
+    public void put(TimeStep step, String key, Object value) {
+        cache.put(key, value);
+        if (step != null) {
+            if (lastStep == null) {
+                lastStep = step;
+            } else if (lastStep.getStep() != step.getStep()) {
+                // if step differ, this indicate new Step
+                changeStep();
+                lastStep = step;
+            }
+        }
+    }
+    
+    @Override
+    public String getStat() {
+        long mean = totalCached / Math.max(1, numberCached);
+        long stepMean = totalStepCached / Math.max(1, numberStepCached);
+
+        double variance = M2/Math.max(1, numberCached - 1);
+        double stepVariance = stepM2/Math.max(1, numberStepCached - 1);
+
+        double standardDeviation = Math.sqrt(variance);
+        double stepStandardDeviation = Math.sqrt(stepVariance);
+
+        return String.format("%s - \n"
+                + "\tmaxMemory: %s, cacheMemory: %s, totalCached: %s, numberStep: %s, numberEntries: %s\n"
+                + "\tStep min: %s, max: %s, mean: %s, standard deviation: %s\n"
+                + "\tEntry min: %s, max: %s, mean: %s, standard deviation: %s\n",
+                getClass().getSimpleName(), 
+                StringUtil.convertMemory(maxMemory), StringUtil.convertMemory(sizeCache), StringUtil.convertMemory(totalCached), numberStepCached, numberCached,
+                StringUtil.convertMemory(smallestStepCached), StringUtil.convertMemory(biggestStepCached), StringUtil.convertMemory(stepMean), StringUtil.convertMemory((long)stepStandardDeviation),
+                StringUtil.convertMemory(smallestCached), StringUtil.convertMemory(biggestCached), StringUtil.convertMemory(mean), StringUtil.convertMemory((long)standardDeviation)
+        );
+    }
+
+
+}

Copied: branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java (from rev 3892, trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java)
===================================================================
--- branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java	                        (rev 0)
+++ branches/4.0.1/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java	2014-03-19 09:51:00 UTC (rev 3893)
@@ -0,0 +1,145 @@
+/*
+ * #%L
+ * IsisFish
+ * 
+ * $Id$
+ * $HeadURL$
+ * %%
+ * Copyright (C) 2006 - 2010 Ifremer, Code Lutin, Cédric Pineau, Benjamin Poussin
+ * %%
+ * 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 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package fr.ifremer.isisfish.util;
+
+import fr.ifremer.isisfish.simulator.SimulationContext;
+import fr.ifremer.isisfish.types.TimeStep;
+import java.util.Map;
+import org.apache.commons.collections.map.ReferenceMap;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+/**
+ * IsisCacheBackendOnReferenceMap utilise pour mettre les resultats de methode durant la simulation
+ pour minimiser les appels
+
+ Created: 25 août 06 22:42:47
+ *
+ * @author poussin
+ * @version $Revision$
+
+ Last update: $Date$
+ by : $Author$
+ */
+public class IsisCacheBackendOnReferenceMap implements IsisCacheBackend {
+    
+    /** to use log facility, just put in your code: log.info(\"...\"); */
+    static private Log log = LogFactory.getLog(IsisCacheBackendOnReferenceMap.class);
+
+    static public class IsisCacheBackendOnReferenceMapFactory implements IsisCacheBackend.Factory {
+        @Override
+        public IsisCacheBackend createNew() {
+            return new IsisCacheBackendOnReferenceMap();
+        }
+    }
+
+    static public Factory factory = new IsisCacheBackendOnReferenceMapFactory();
+
+    // la longueur du package pour minimiser la longueur des topiaId
+    static final private int entityPackageLenght = "fr.ifremer.isisfish.entities.".length();
+    // la valeur NULL a utilise a la place de null pour les timeStep
+    static final private Object NULL = new Object();
+
+    /**
+     * map<TimeStep, Map<Key, Value>>
+     * TimeStep peut etre null via l'objet NULL
+     * Key est la cle calcule par computeKey
+     * Value est la valeur du cache
+     *
+     * TimeStep est en WEAK pour que des que l'on passe au pas de temps suivant
+     * ils soit efface de la memoire si plus personne n'a de reference sur
+     * ce pas de temps. L'autre moyen est de force l'effacement via clear(TimeStep)
+     *
+     * Value est en SOFT reference pour que les valeurs soit effacee du cache
+     * lorsqu'il n'y a plus de place memoire
+     */
+    protected Map cache = new ReferenceMap(ReferenceMap.WEAK, ReferenceMap.HARD);
+    
+    public IsisCacheBackendOnReferenceMap() {
+    }
+
+    /**
+     * Return trace object from context.
+     *
+     * @return trace object from context
+     */
+    protected Trace getTrace() {
+        SimulationContext context = SimulationContext.get();
+        Trace result = context.getTrace();
+        return result;
+    }
+
+    protected Map getCacheTimeStep(TimeStep step) {
+        Object key = step;
+        if (step == null)  {
+            key = NULL;
+        }
+        Map result = (Map)cache.get(key);
+        if (result == null) {
+            result = new ReferenceMap(ReferenceMap.HARD, ReferenceMap.SOFT);
+            cache.put(key, result);
+        }
+        return result;
+    }
+
+    @Override
+    public Object get(TimeStep step, String key) {
+        Object result = null;
+        Map cacheTimeStep = getCacheTimeStep(step);
+        if (cacheTimeStep != null) {
+            result = cacheTimeStep.get(key);
+        }
+        return result;
+    }
+
+    @Override
+    public void put(TimeStep step, String key, Object value) {
+        getCacheTimeStep(step).put(key, value);
+    }
+
+    /**
+     * remove all values in cache
+     */
+    @Override
+    public void clear() {
+        cache.clear();
+    }
+
+    /**
+     * remove all values in cache for the specied TimeStep
+     */
+    @Override
+    public void removeStep(Object o) {
+        cache.remove(o);
+    }
+
+    @Override
+    public String getStat() {
+        return String.format("%s - no specific stat\n", getClass().getSimpleName());
+    }
+}
+
+

Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties
===================================================================
--- branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/resources/i18n/isis-fish_en_GB.properties	2014-03-19 09:51:00 UTC (rev 3893)
@@ -164,6 +164,7 @@
 isisfish.common.warn=warn
 isisfish.common.year=year
 isisfish.common.zone=Zone
+isisfish.config.cache.backend.factory.class.description=Cache backend class to use for simulation
 isisfish.config.category.communityvcs=Community VCS
 isisfish.config.category.communityvcs.description=Community VCS repository
 isisfish.config.category.main=Main

Modified: branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties
===================================================================
--- branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/resources/i18n/isis-fish_fr_FR.properties	2014-03-19 09:51:00 UTC (rev 3893)
@@ -164,6 +164,7 @@
 isisfish.common.warn=Warning
 isisfish.common.year=année
 isisfish.common.zone=Zone
+isisfish.config.cache.backend.factory.class.description=Implantation du cache à utiliser pour les simulations
 isisfish.config.category.communityvcs=VCS Communauté
 isisfish.config.category.communityvcs.description=Dépôt contenant les scripts de la communautés
 isisfish.config.category.main=Globale
@@ -981,12 +982,12 @@
 isisfish.strategy.inactivity=Equation d'inactivité
 isisfish.strategy.inactivityEquationUsed=Utiliser une équation d'inactivité
 isisfish.strategy.name=Nom
-isisfish.strategy.proportionMetier=Proportion metier
-isisfish.strategy.proportionMetierLabel=Proportion metier \:
+isisfish.strategy.proportionMetier=Proportion métier
+isisfish.strategy.proportionMetierLabel=Proportion métier \:
 isisfish.strategy.proportionSetOfVessels=Proportion de la flottille
 isisfish.strategy.title=Caractéristiques
 isisfish.strategyMonthInfo.metier=Métier
-isisfish.strategyMonthInfo.minInactivityDays=Jour minimums d'inactivité
+isisfish.strategyMonthInfo.minInactivityDays=Jours minimums d'inactivité
 isisfish.strategyMonthInfo.numberOfTrips=Nombre de trajets
 isisfish.strategyMonthInfo.proportion=Proportion
 isisfish.strategyMonthInfo.title=Saisie des mois

Modified: branches/4.0.1/src/main/resources/sensitivity.properties
===================================================================
--- branches/4.0.1/src/main/resources/sensitivity.properties	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/resources/sensitivity.properties	2014-03-19 09:51:00 UTC (rev 3893)
@@ -42,6 +42,7 @@
 Population.groupMin
 Population.growth
 Population.growthReverse
+Population.mappingZoneReproZoneRecru
 Population.maturityOgiveEquation
 Population.meanWeight
 Population.monthGapBetweenReproRecrutement
@@ -54,6 +55,7 @@
 PopulationSeasonInfo.migrationEquation
 PopulationSeasonInfo.emigrationEquation
 PopulationSeasonInfo.immigrationEquation
+PopulationSeasonInfo.reproductionDistribution
 Selectivity.equation
 SetOfVessels.fixedCosts
 SetOfVessels.numberOfVessels

Modified: branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl
===================================================================
--- branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl	2014-03-19 09:16:24 UTC (rev 3892)
+++ branches/4.0.1/src/main/resources/templates/ssh/qsub-script.ftl	2014-03-19 09:51:00 UTC (rev 3893)
@@ -5,7 +5,7 @@
  $Id$
  $HeadURL$
  %%
- Copyright (C) 2009 - 2012 Ifremer, CodeLutin, Chatellier Eric
+ Copyright (C) 2009 - 2014 Ifremer, CodeLutin, Chatellier Eric
  %%
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as
@@ -29,7 +29,7 @@
 setenv R_HOME /appli/R/2.15.0-gnu-4.3/lib64/R
 setenv LD_LIBRARY_PATH ${r"${R_HOME}"}/lib
 
-<#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx${javamemory} -jar isis-fish*.jar" />
+<#assign commonCommand="${javapath} -Djava.library.path=jri64 -DR.type=jni -Xmx${javamemory} -XX:+UseSerialGC -jar isis-fish*.jar" />
 <#assign commonOptions="--option launch.ui false --option perform.vcsupdate false --option perform.migration false --option perform.cron false" />
 <#if qsubmutiplejob>
 	<#-- localsimulationid is short simulation id version -->

    

echatellier＠users.forge.codelutin.com

tags

participants (1)