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r4039 - trunk/src/main/java/fr/ifremer/isisfish/simulator
by bpoussin＠users.forge.codelutin.com July 16, 2014

July 16, 2014

Author: bpoussin Date: 2014-07-16 22:45:26 +0200 (Wed, 16 Jul 2014) New Revision: 4039 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4039 Log: add dimension name in initial N Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java 2014-07-11 15:35:04 UTC (rev 4038) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationParameterImpl.java 2014-07-16 20:45:26 UTC (rev 4039) @@ -76,6 +76,8 @@ import fr.ifremer.isisfish.rule.RuleHelper; import fr.ifremer.isisfish.simulator.sensitivity.SensitivityAnalysis; +import static org.nuiton.i18n.I18n.n; + /** * Real {@link SimulationParameter} implementation. * @@ -315,7 +317,10 @@ zones.add("No zone"); } List[] semantics = new List[] { groups, zones }; - result = MatrixFactory.getInstance().create(semantics); + result = MatrixFactory.getInstance().create( + n("matrixAbundance"), + semantics, + new String[] { n("Groups"), n("Zones") }); numbers.put(pop, result); }

1 0

r4038 - in trunk: . src/license src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: bpoussin Date: 2014-07-11 17:35:04 +0200 (Fri, 11 Jul 2014) New Revision: 4038 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4038 Log: - add license header - use nuiton-matrix 2.5-SNAPSHOT Modified: trunk/pom.xml trunk/src/license/THIRD-PARTY.properties trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/pom.xml 2014-07-11 15:35:04 UTC (rev 4038) @@ -88,14 +88,14 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.4.2-SNAPSHOT</version> + <version>2.5-SNAPSHOT</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix-gui</artifactId> - <version>2.4.2-SNAPSHOT</version> + <version>2.5-SNAPSHOT</version> <scope>compile</scope> </dependency> Modified: trunk/src/license/THIRD-PARTY.properties =================================================================== --- trunk/src/license/THIRD-PARTY.properties 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/license/THIRD-PARTY.properties 2014-07-11 15:35:04 UTC (rev 4038) @@ -45,9 +45,8 @@ # Please fill the missing licenses for dependencies : # # -#Fri May 30 10:59:27 CEST 2014 +#Fri Jul 11 17:44:59 CEST 2014 commons-jxpath--commons-jxpath--1.3=The Apache Software License, Version 2.0 commons-primitives--commons-primitives--1.0=The Apache Software License, Version 2.0 dom4j--dom4j--1.6.1=BSD License -javax.activation--activation--1.1.1=COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 org.antlr--antlr-runtime--3.4=BSD License Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -1,6 +1,28 @@ package fr.ifremer.isisfish.datastore; +/* + * #%L + * IsisFish + * %% + * Copyright (C) 1999 - 2014 Ifremer, Codelutin + * %% + * 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% + */ + import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.simulator.SimulationContext; Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/sensitivity/wizard/ContinuousDistributionPanel.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2012, 2014 Ifremer, Codelutin, Chatellier Eric + * Copyright (C) 2012 - 2014 Ifremer, Codelutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as Modified: trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java 2014-07-11 11:21:35 UTC (rev 4037) +++ trunk/src/main/java/fr/ifremer/isisfish/util/SimpleParser.java 2014-07-11 15:35:04 UTC (rev 4038) @@ -1,6 +1,28 @@ package fr.ifremer.isisfish.util; +/* + * #%L + * IsisFish + * %% + * Copyright (C) 1999 - 2014 Ifremer, Codelutin + * %% + * 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% + */ + import java.io.BufferedReader; import java.io.IOException; import org.apache.commons.logging.Log;

1 0

r4037 - in trunk/src/main: java/fr/ifremer/isisfish java/fr/ifremer/isisfish/simulator java/fr/ifremer/isisfish/ui resources/i18n
by bpoussin＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: bpoussin Date: 2014-07-11 13:21:35 +0200 (Fri, 11 Jul 2014) New Revision: 4037 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4037 Log: - can use Lazy or not via configuration Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java trunk/src/main/resources/i18n/isis-fish_en_GB.properties trunk/src/main/resources/i18n/isis-fish_fr_FR.properties Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -846,6 +846,8 @@ getOption(Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS.key)); result.put(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key, getOption(Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS.key)); + result.put(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key, + getOption(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key)); result.put(Option.SIMULATION_STORE_RESULT_ON_DISK.key, getOption(Option.SIMULATION_STORE_RESULT_ON_DISK.key)); result.put(Option.SIMULATION_STORE_RESULT_CACHE_STEP.key, @@ -1010,6 +1012,18 @@ } /** + * Seuil d'uitilisation des matrices creuse + * + * @return + * @since 4.3.1.0 + */ + public boolean getSimulationMatrixdUseLazyVector() { + ApplicationConfig config = SimulationContext.get().getConfig(); + boolean result = config.getOptionAsBoolean(Option.SIMULATION_MATRIX_USE_LAZY_VECTOR.key); + return result; + } + + /** * Indique le nombre de pas qui doivent etre sauve, en partant du dernier pas * de temps. * @@ -1083,6 +1097,7 @@ SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.class.getName()), SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleSparseHashVector.class.getName()), SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS("simulation.matrix.threshold.use.sparse.class", n("isisfish.config.simulation.matrix.threshold.use.sparse.class.description"), "1000"), + SIMULATION_MATRIX_USE_LAZY_VECTOR("simulation.matrix.use.lazy.vector", n("isisfish.config.simulation.matrix.use.lazy.vector.description"), "true"), SIMULATION_STORE_RESULT_ON_DISK("simulation.store.result.ondisk", n("isisfish.config.simulation.store.result.ondisk.description"), "-1"), SIMULATION_STORE_RESULT_CACHE_STEP("simulation.store.result.cachestep", n("isisfish.config.simulation.store.result.cachestep.description"), "13"), Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -131,7 +131,8 @@ MatrixFactory.initMatrixFactoryThreadLocal( IsisFish.config.getSimulationMatrixVectorClass(), IsisFish.config.getSimulationMatrixVectorSparseClass(), - IsisFish.config.getSimulationMatrixThresholdUseSparse()); + IsisFish.config.getSimulationMatrixThresholdUseSparse(), + IsisFish.config.getSimulationMatrixdUseLazyVector()); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/WelcomeHandler.java 2014-07-11 11:21:35 UTC (rev 4037) @@ -228,6 +228,7 @@ modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_VECTOR_SPARSE_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS); + modelBuilder.addOption(IsisConfig.Option.SIMULATION_MATRIX_USE_LAZY_VECTOR); modelBuilder.addOption(IsisConfig.Option.MAPPED_RESULT_MATRIX_VECTOR_CLASS); modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_ON_DISK); modelBuilder.addOption(IsisConfig.Option.SIMULATION_STORE_RESULT_CACHE_STEP); Modified: trunk/src/main/resources/i18n/isis-fish_en_GB.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/resources/i18n/isis-fish_en_GB.properties 2014-07-11 11:21:35 UTC (rev 4037) @@ -230,6 +230,7 @@ isisfish.config.main.userName.description=User name isisfish.config.mapped.result.matrix.vector.class.description= isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.use.lazy.vector.description= isisfish.config.simulation.matrix.vector.class.description= isisfish.config.simulation.matrix.vector.sparse.class.description= isisfish.config.simulation.store.result.cachestep.description= Modified: trunk/src/main/resources/i18n/isis-fish_fr_FR.properties =================================================================== --- trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-11 08:50:40 UTC (rev 4036) +++ trunk/src/main/resources/i18n/isis-fish_fr_FR.properties 2014-07-11 11:21:35 UTC (rev 4037) @@ -230,6 +230,7 @@ isisfish.config.main.userName.description=le nom - prénom de l'utilisateur isisfish.config.mapped.result.matrix.vector.class.description= isisfish.config.simulation.matrix.threshold.use.sparse.class.description= +isisfish.config.simulation.matrix.use.lazy.vector.description= isisfish.config.simulation.matrix.vector.class.description= isisfish.config.simulation.matrix.vector.sparse.class.description= isisfish.config.simulation.store.result.cachestep.description=

1 0

r4036 - trunk
by echatellier＠users.forge.codelutin.com July 11, 2014

July 11, 2014

Author: echatellier Date: 2014-07-11 10:50:40 +0200 (Fri, 11 Jul 2014) New Revision: 4036 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4036 Log: Update libs Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-10 23:17:57 UTC (rev 4035) +++ trunk/pom.xml 2014-07-11 08:50:40 UTC (rev 4036) @@ -20,7 +20,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-utils</artifactId> - <version>3.0-rc-3</version> + <version>3.0-rc-4</version> <scope>compile</scope> </dependency> @@ -290,7 +290,7 @@ <dependency> <groupId>org.aspectj</groupId> <artifactId>aspectjweaver</artifactId> - <version>1.8.0</version> + <version>1.8.1</version> </dependency> <dependency> @@ -312,7 +312,7 @@ <dependency> <groupId>org.tmatesoft.svnkit</groupId> <artifactId>svnkit</artifactId> - <version>1.8.3-1</version> + <version>1.8.5</version> <scope>compile</scope> </dependency>  @@ -327,7 +327,7 @@ <dependency> <groupId>org.eclipse.jdt.core.compiler</groupId> <artifactId>ecj</artifactId> - <version>4.3.1</version> + <version>4.4</version> </dependency> <dependency> @@ -483,7 +483,7 @@  <jaxxVersion>2.8.7</jaxxVersion> <eugeneVersion>2.7.4</eugeneVersion> - <topiaVersion>2.9-rc-1</topiaVersion> + <topiaVersion>2.9.1</topiaVersion> <hibernateVersion>4.3.5.Final</hibernateVersion> <nuitonI18nVersion>3.1</nuitonI18nVersion> <nuitonWidgetsVersion>1.1.1</nuitonWidgetsVersion>

1 0

r4035 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 10, 2014

July 10, 2014

Author: bpoussin Date: 2014-07-11 01:17:57 +0200 (Fri, 11 Jul 2014) New Revision: 4035 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4035 Log: remove old code Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 16:41:47 UTC (rev 4034) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 23:17:57 UTC (rev 4035) @@ -109,7 +109,7 @@ Object result; - if (Void.TYPE == method.getReturnType()) { + if (Void.TYPE.equals(method.getReturnType())) { // for void return type, never put it in cache, we can call directly real method result = realCall(defaultValue); } else { @@ -140,16 +140,10 @@ 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); // si return null on stock NULL pour faire la distinction // entre present dans le cache ou absent (get(...) return null) -// if (returnType != != 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==null?NULL:result); -// } } else { if (result == NULL) { result = null;

1 0

r4034 - trunk
by echatellier＠users.forge.codelutin.com July 10, 2014

July 10, 2014

Author: echatellier Date: 2014-07-10 18:41:47 +0200 (Thu, 10 Jul 2014) New Revision: 4034 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4034 Log: Update snapshot Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-10 16:35:38 UTC (rev 4033) +++ trunk/pom.xml 2014-07-10 16:41:47 UTC (rev 4034) @@ -81,7 +81,7 @@ <dependency> <groupId>org.nuiton</groupId> <artifactId>nuiton-profiling</artifactId> - <version>2.7.2-SNAPSHOT</version> + <version>3.0-SNAPSHOT</version> <scope>compile</scope> </dependency>

1 0

r4033 - in trunk: . src/main/java/fr/ifremer/isisfish src/main/java/fr/ifremer/isisfish/datastore src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com July 10, 2014

July 10, 2014

Author: bpoussin Date: 2014-07-10 18:35:38 +0200 (Thu, 10 Jul 2014) New Revision: 4033 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4033 Log: - change version to 4.3.1.0 - add information on each step (min, max, mean, ...) - rewrite IsisCache method for performance - sumOverDim use semantics 1,2,3,4,... for new dimensions Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationListener.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationResultXML.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/pom.xml 2014-07-10 16:35:38 UTC (rev 4033) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.0.2-SNAPSHOT</version> + <version>4.3.1.0-SNAPSHOT</version>  <dependencies> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -122,7 +122,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 3, 0, 2); + protected final static Version version = new Version(4, 3, 1, 0); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version( Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -843,6 +843,10 @@ public void beforeSimulation(SimulationContext context) { } + @Override + public void stepChange(SimulationContext context, TimeStep step) { + } + // public void addActivatedRule(ResultStorage self, Date date, RegleParam rule){ // List rules = (List)activatedRules.get(date); // if(rules == null){ Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -698,6 +698,10 @@ public void beforeSimulation(SimulationContext context) { } + @Override + public void stepChange(SimulationContext context, TimeStep step) { + } + // public void addActivatedRule(ResultStorage self, Date date, RegleParam rule){ // List rules = (List)activatedRules.get(date); // if(rules == null){ Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -42,6 +42,8 @@ import fr.ifremer.isisfish.simulator.sensitivity.SensitivityUtils; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.IsisCache; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; //import fr.ifremer.isisfish.util.Trace; import org.nuiton.config.ApplicationConfig; import org.nuiton.config.OverwriteApplicationConfig; @@ -82,6 +84,13 @@ protected RuleMonitor ruleMonitor = null; protected ResultManager resultManager = null; protected Set<SimulationListener> simulationListeners = new LinkedHashSet<SimulationListener>(); + protected PropertyChangeListener stepListener = new PropertyChangeListener() { + @Override + public void propertyChange(PropertyChangeEvent evt) { + SimulationContext.this.fireStepChange(new TimeStep((Integer)evt.getNewValue())); + } + }; + protected ClassLoader classLoader = null; protected File scriptDirectory; /** l'objet trace qui conserve les donnees statistiques des appels de methodes */ @@ -227,6 +236,12 @@ } } + public void fireStepChange(TimeStep step) { + for (SimulationListener l : simulationListeners) { + l.stepChange(this, step); + } + } + public void fireAfterSimulation() { for (SimulationListener l : simulationListeners) { l.afterSimulation(this); @@ -306,7 +321,15 @@ * @param simulationControl The simulationControl to set. */ public void setSimulationControl(SimulationControl simulationControl) { - this.simulationControl = simulationControl; + if (this.simulationControl != simulationControl) { + if (this.simulationControl != null) { + this.simulationControl.removePropertyChangeListener("step", stepListener); + } + this.simulationControl = simulationControl; + if (simulationControl != null) { + simulationControl.addPropertyChangeListener("step", stepListener); + } + } } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationExportResultWrapper.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -32,7 +32,6 @@ import java.util.List; import java.util.Set; -import org.apache.commons.collections4.ListUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -42,6 +41,7 @@ import fr.ifremer.isisfish.export.Export; import fr.ifremer.isisfish.export.ExportHelper; import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.TimeStep; /** * Export simulation listener. @@ -125,4 +125,8 @@ @Override public void beforeSimulation(SimulationContext context) { } + + @Override + public void stepChange(SimulationContext context, TimeStep step) { + } } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationListener.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationListener.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationListener.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -25,6 +25,8 @@ package fr.ifremer.isisfish.simulator; +import fr.ifremer.isisfish.types.TimeStep; + /** * You can create new SimulationListener and add it for simulation. To do that * add tag/value in advanced parameter simulation launcher like @@ -44,6 +46,14 @@ public void beforeSimulation(SimulationContext context); /** + * Receive event when simulation change step + * + * @param context + * @param step + */ + public void stepChange(SimulationContext context, TimeStep step); + + /** * called after simulation * * @param context Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationPreScriptListener.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -27,13 +27,11 @@ import static org.nuiton.i18n.I18n.t; -import java.util.HashMap; -import java.util.Map; - import org.apache.commons.lang3.StringUtils; import org.nuiton.topia.TopiaContext; import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.EvaluatorHelper; /** @@ -93,4 +91,8 @@ t("Can't evaluate simulation prescript"), eee); } } + + @Override + public void stepChange(SimulationContext context, TimeStep step) { + } } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationResultXML.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationResultXML.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationResultXML.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -164,6 +164,10 @@ } + @Override + public void stepChange(SimulationContext context, TimeStep step) { + } + } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -71,6 +71,8 @@ import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.CompileHelper; import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.profiling.Statistic; +import org.nuiton.profiling.Unit; /** * Fait une simulation dans la meme jvm. @@ -87,7 +89,45 @@ private static Log log = LogFactory .getLog(InProcessSimulatorLauncher.class); + protected static class StepTimeStat implements SimulationListener { + + protected long lastTime = 0; + protected Statistic stat = new Statistic("Step time"){ + @Override + public String formatValue(long value) { + String result = String.valueOf(Unit.Time.nano.convertTo(Unit.Time.s, value)); + return result; + } + }; + + public Statistic getStat() { + return stat; + } + + @Override + public void beforeSimulation(SimulationContext context) { + } + + @Override + public void stepChange(SimulationContext context, TimeStep step) { + if (lastTime == 0) { + lastTime = System.nanoTime(); + } else { + long newTime = System.nanoTime(); + long delta = newTime - lastTime; + lastTime = newTime; + stat.add(delta); + } + } + + @Override + public void afterSimulation(SimulationContext context) { + } + + } + protected SimulationStorage simulation; + protected StepTimeStat stepTimeStat = new StepTimeStat(); /** * {@inheritDoc} @@ -434,6 +474,9 @@ + matrixBackend + " and " + matrixSparseBackend + " threshold: " + threshold); simulatorObject.simulate(context); + simulation.getInformation().addInformation( + stepTimeStat.getStat().exportText(null).toString()); + // // Ajout des nouveaux objets créés durant la simulation // @@ -545,6 +588,9 @@ // - ResultStorage context.addSimulationListener(simulation.getResultStorage()); + // ajout du listener de statistique sur le temps de chaque pas de temps + context.addSimulationListener(stepTimeStat); + // - TODO: mexico xml result // - TODO: vle result String simListener = context.getSimulationStorage().getParameter() Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 12:25:39 UTC (rev 4032) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 16:35:38 UTC (rev 4033) @@ -31,7 +31,6 @@ import org.aspectj.lang.ProceedingJoinPoint; import org.nuiton.topia.persistence.TopiaEntity; -import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; import java.util.HashMap; import java.util.Map; @@ -60,7 +59,7 @@ // 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 + // la valeur NULL a utilise a la place de null pour les timeStep, et les retours de method static final private Object NULL = new Object(); protected long totalCall = 0; @@ -108,44 +107,55 @@ public Object get(Method method, Object[] args, Object defaultValue) throws Throwable { totalCall++; - Object result = null; + Object result; - String methodString = methodStringCache.get(method); - if (methodString == null) { - Class declaringClass = method.getDeclaringClass(); - methodString = (method.getAnnotation(Nocache.class) != null - || declaringClass.getAnnotation(Nocache.class) != null)? - "@" : ""; - methodString += declaringClass.getSimpleName() + "."+ method.getName(); - methodString = methodString.intern(); - methodStringCache.put(method, methodString); - } - - // if method have annotation 'noCache' name start with @ - if (methodString.charAt(0) == '@') { + if (Void.TYPE == method.getReturnType()) { + // for void return type, never put it in cache, we can call directly real method result = realCall(defaultValue); } else { - // compute key and keep TimeStep objet - // le pas de temps trouve dans les arguments - sbKey.setLength(0); - TimeStep step = computeKey(sbKey, methodString, 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) { + String methodString = methodStringCache.get(method); + if (methodString == null) { + Class declaringClass = method.getDeclaringClass(); + methodString = (method.getAnnotation(Nocache.class) != null + || declaringClass.getAnnotation(Nocache.class) != null)? + "@" : ""; + methodString += declaringClass.getSimpleName() + "."+ method.getName(); + methodString = methodString.intern(); + methodStringCache.put(method, methodString); + } - // computation increment (/ by 0) - // FIXME need to be called, but fail with empty stack - //getTrace().traceAfterComputation(method); + // if method have annotation 'noCache' name start with @ + if (methodString.charAt(0) == '@') { 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 { + // compute key and keep TimeStep objet + // le pas de temps trouve dans les arguments + sbKey.setLength(0); + TimeStep step = computeKey(sbKey, methodString, 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); + // si return null on stock NULL pour faire la distinction + // entre present dans le cache ou absent (get(...) return null) +// if (returnType != != 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==null?NULL:result); +// } + } else { + if (result == NULL) { + result = null; + } + cacheUsed++; } - } else { - cacheUsed++; } } return result;

1 0

r4032 - in trunk/src/main/java/fr/ifremer/isisfish: datastore entities types util
by bpoussin＠users.forge.codelutin.com July 10, 2014

July 10, 2014

Author: bpoussin Date: 2014-07-10 14:25:39 +0200 (Thu, 10 Jul 2014) New Revision: 4032 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4032 Log: optimisation Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationGroupImpl.java trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageAbstract.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -120,11 +120,11 @@ // interne avant de l'utiliser comme cle. internalValue = internalValue.intern(); result = internalValue; - if (StringUtils.startsWith(internalValue, Month.class.getName())) { + if (StringUtils.startsWith(internalValue, "Month")) { String val = StringUtils.substringAfter(internalValue, SEP); int monthNumber = Integer.parseInt(val); - result = new Month(monthNumber); - } else if (StringUtils.startsWith(internalValue, TimeStep.class.getName())) { + result = Month.MONTH[monthNumber]; + } else if (StringUtils.startsWith(internalValue, "TimeStep")) { String val = StringUtils.substringAfter(internalValue, SEP); int stepNumber = Integer.parseInt(val); result = new TimeStep(stepNumber); @@ -155,9 +155,9 @@ String result = cache.getKey(decoratedValue); if (result == null && decoratedValue != null) { if (decoratedValue instanceof Month) { - result = Month.class.getName() + SEP + ((Month)decoratedValue).getMonthNumber(); + result = "Month" + SEP + ((Month)decoratedValue).getMonthNumber(); } else if (decoratedValue instanceof TimeStep) { - result = TimeStep.class.getName() + SEP + ((TimeStep)decoratedValue).getStep(); + result = "TimeStep" + SEP + ((TimeStep)decoratedValue).getStep(); } else if (decoratedValue instanceof TopiaEntity) { result = ((TopiaEntity)decoratedValue).getTopiaId() + SEP + decoratedValue; } else { Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorageCSV.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -21,6 +21,7 @@ import java.util.Arrays; import java.util.Collections; import java.util.HashMap; +import java.util.HashSet; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -67,10 +68,6 @@ * 0;2;1;4.2 * </pre> * - * TODO: - * stat du nombre de demande de resultat or pas de temps courant - * stat sur max ecart entre pas de temps courant et pas de temps demande - * * @author poussin * @version $Revision$ * @@ -89,14 +86,27 @@ /** number of step in cache */ protected int cacheStep = 13; // default to 13 months + /** Le pas de temps a partir duquel il faut sauver les resultats sur disque*/ + protected TimeStep startDiskStep = null; + + /** use to prevent to much call */ + private File directoryCache; + /** nombre total de resultat */ protected int numberOfResult = 0; /** nombre de resultat reellement stocke sur disque */ protected int numberOfResultOnDisk = 0; - /** le nombre de resultat demande qui n'etait pas dans le pas de temps courant */ - protected int numberOfPastResultAsked = 0; - /** le plus vieux pas de temps demande par rapport au pas de temps courant */ - protected int maxGapWithCurrentStep = 0; + /** le nombre de resultat demande */ + protected int numberOfResultAsked = 0; + /** le nombre de resultat lu dans le cache */ + protected int numberOfResultReadInCache = 0; + /** le nombre de resultat lu sur le disque */ + protected int numberOfResultReadOnDisk = 0; + /** + * le plus vieux pas de temps demande par rapport au pas de temps courant + * lu sur le disque + */ + protected int maxGapWithCurrentStepReadOnDisk = 0; LinkedHashMap<TimeStep, Map<String, MatrixND>> cache = new LinkedHashMap<TimeStep, Map<String, MatrixND>>() { @@ -107,7 +117,6 @@ } }; - public ResultStorageCSV(SimulationStorage simulation) { super(simulation); @@ -120,9 +129,11 @@ return String.format( "ResultStorageCSV:\n" + "\t%s results written to disk on a total of %s\n" - + "\t%s results read outside of current step\n" - + "\tthe oldest step was %s step before current step\n", - numberOfResultOnDisk, numberOfResult, numberOfPastResultAsked, maxGapWithCurrentStep); + + "\t%s results read (%s in cache and %s on disk)\n" + + "\tthe oldest step read on disk was %s step before current step\n", + numberOfResultOnDisk, numberOfResult, + numberOfResultAsked, numberOfResultReadInCache, numberOfResultReadOnDisk, + maxGapWithCurrentStepReadOnDisk); } /** @@ -130,8 +141,10 @@ * @return */ protected File getDirectory() { - File file = SimulationStorage.getResultDirectory(simulation.getDirectory()); - return file; + if (directoryCache == null) { + directoryCache = SimulationStorage.getResultDirectory(simulation.getDirectory()); + } + return directoryCache; } /** @@ -149,6 +162,34 @@ return file; } + protected HashSet<String> fileExistCache; + protected HashSet<String> getFileExistCache() { + if (fileExistCache == null) { + fileExistCache = new HashSet<String>(); + File matrixDir = getMatrixDirectory(""); + File[] resultDirs = matrixDir.listFiles(); + if (resultDirs != null) { + for (File resultDir : resultDirs) { + + Collections.addAll(fileExistCache, resultDir.list()); + } + } + } + return fileExistCache; + } + /** + * Method used to know if file result exist. Usage of File.exists take to long time + * during simulation + * @param f + * @return + */ + protected boolean fileExist(File f) { + return getFileExistCache().contains(f.getName()); + } + protected void addFileExist(File f) { + getFileExistCache().add(f.getName()); + } + protected MatrixND readMatrix(String file) throws IOException { MatrixND result = null; LineNumberReader in = null; @@ -227,6 +268,7 @@ try { File file = getDirectory(); FileUtils.deleteDirectory(file); + fileExistCache = null; } catch (IOException eee) { throw new IsisFishRuntimeException("Can't delete results", eee); } @@ -235,14 +277,7 @@ @Override protected MatrixND readResult(TimeStep step, String name) { // un peu de statistique (seulement en simulation - SimulationControl sc = SimulationContext.get().getSimulationControl(); - if (sc != null) { - TimeStep currentStep = sc.getStep(); - if (!step.equals(currentStep)) { - numberOfPastResultAsked++; - maxGapWithCurrentStep = Math.max(maxGapWithCurrentStep, currentStep.gap(step)); - } - } + numberOfResultAsked++; MatrixND result = null; @@ -252,11 +287,23 @@ } // if not found looking for result on disk - if (result == null) { + if (result != null) { + numberOfResultReadInCache++; + } else { File file = getMatrixFile(step, name); - if (file.exists()) { + if (fileExist(file)) { try { result = readMatrix(file.getPath()); + + // un peu de statistique (seulement en simulation + numberOfResultReadOnDisk++; + SimulationControl sc = SimulationContext.get().getSimulationControl(); + if (sc != null) { + TimeStep currentStep = sc.getStep(); + if (!step.equals(currentStep)) { + maxGapWithCurrentStepReadOnDisk = Math.max(maxGapWithCurrentStepReadOnDisk, currentStep.gap(step)); + } + } } catch (IOException eee) { log.error("Can't read result file: " + file, eee); } @@ -287,9 +334,6 @@ // return result; // } - /** Le pas de temps a partir duquel il faut sauver les resultats sur disque*/ - protected TimeStep startDiskStep = null; - /** * Indique s'il faut sauver sur disque les resultats * @param step @@ -370,6 +414,8 @@ out.println(); } + // result file is writen without error, add it to fileExistCache + addFileExist(file); } catch (Exception eee) { throw new IsisFishRuntimeException("Can't write result: " + file, eee); } finally { Modified: trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationGroupImpl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationGroupImpl.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/entities/PopulationGroupImpl.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -199,10 +199,18 @@ } return result; } - + + private String toStringCache; @Override public String toString() { - return t("isisfish.populationGroup.toString", this.getPopulation(), - this.getId()); + // trop couteux d'appeler i18n, appele des millions de fois + // et est vraiment raisonnable d'avoir des string != suivant le langage + // quel impact dans les scripts utilisateurs ? +// return t("isisfish.populationGroup.toString", this.getPopulation(), +// this.getId()); + if (toStringCache == null) { + toStringCache = this.getPopulation().toString() + " Group " + this.getId(); + } + return toStringCache; } } Modified: trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/types/TimeStep.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -178,6 +178,7 @@ return this.step >= d.step; } + @Override public boolean equals(Object o) { if (o instanceof TimeStep) { return step == ((TimeStep) o).step; @@ -185,6 +186,7 @@ return false; } + @Override public int hashCode() { return step; } Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -33,6 +33,8 @@ import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.types.TimeStep; +import java.util.HashMap; +import java.util.Map; /** * IsisCacheOnReferenceMap utilise pour mettre les resultats de methode durant @@ -86,6 +88,15 @@ // } /** + * La representation de la methode en string, la representation commence + * par un @ si il y a l'annotation noCache trouver pour cette methode. + */ + protected Map<Method, String> methodStringCache = new HashMap<Method, String>(); + // use to compute key, isis simulation is monothread, we can instanciate it here + // to minimise object instanciation + protected StringBuilder sbKey = new StringBuilder(300); + + /** * Recupere pour un pas de temps donnes une valeur calcule pour une cle. * * @param defaultValue la valeur par defaut a retourner si elle n'est pas en @@ -98,14 +109,26 @@ totalCall++; Object result = null; - if (method.getAnnotation(Nocache.class) != null - || method.getDeclaringClass().getAnnotation(Nocache.class) != null) { + + String methodString = methodStringCache.get(method); + if (methodString == null) { + Class declaringClass = method.getDeclaringClass(); + methodString = (method.getAnnotation(Nocache.class) != null + || declaringClass.getAnnotation(Nocache.class) != null)? + "@" : ""; + methodString += declaringClass.getSimpleName() + "."+ method.getName(); + methodString = methodString.intern(); + methodStringCache.put(method, methodString); + } + + // if method have annotation 'noCache' name start with @ + if (methodString.charAt(0) == '@') { 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); + sbKey.setLength(0); + TimeStep step = computeKey(sbKey, methodString, args); // on recupere le intern de la String car normalement en cache on // retrouve souvent les memes chaines comme cle (sinon le cache @@ -128,11 +151,9 @@ return result; } - protected TimeStep computeKey(StringBuilder sbKey, Method method, Object[] args) { + protected TimeStep computeKey(StringBuilder sbKey, String methodString, Object[] args) { TimeStep result = null; - sbKey.append(method.getDeclaringClass().getSimpleName()); - sbKey.append("."); - sbKey.append(method.getName()); + sbKey.append(methodString); for (Object o : args) { sbKey.append(";"); if (o == null) { @@ -141,7 +162,7 @@ sbKey.append(o.toString()); } else if (o instanceof TimeStep) { result = (TimeStep) o; - sbKey.append(((TimeStep) o).getStep()); + sbKey.append(result.getStep()); } else if (o instanceof TopiaEntity) { sbKey.append(((TopiaEntity) o).getTopiaId().substring(entityPackageLenght)); } else { @@ -149,7 +170,7 @@ sbKey.append(o.getClass().getSimpleName()); sbKey.append('@'); // et en lui ajoutant son adresse memoire en Hexa - sbKey.append(Integer.toHexString(System.identityHashCode(o))); + sbKey.append(System.identityHashCode(o)); } } return result; Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-07-08 17:24:51 UTC (rev 4031) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnGuava.java 2014-07-10 12:25:39 UTC (rev 4032) @@ -292,15 +292,24 @@ double standardDeviation = Math.sqrt(variance); double stepStandardDeviation = Math.sqrt(stepVariance); - return String.format("%s - \n" + String trick = ""; + if (sizeCache < biggestStepCached) { + trick = String.format( + "TRICK: for better performance you must set memory at least to %s\n", + StringUtil.convertMemory(biggestStepCached + 500 * 1024 *1024)); + } + String result = String.format("%s - \n%s" + "\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", + trick, 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) ); + + return result; }

1 0

r4031 - in trunk: . src/main/java/fr/ifremer/isisfish/aspect src/main/java/fr/ifremer/isisfish/entities src/main/java/fr/ifremer/isisfish/simulator src/main/java/fr/ifremer/isisfish/simulator/launcher src/main/java/fr/ifremer/isisfish/util src/main/xmi
by bpoussin＠users.forge.codelutin.com July 8, 2014

July 8, 2014

Author: bpoussin Date: 2014-07-08 19:24:51 +0200 (Tue, 08 Jul 2014) New Revision: 4031 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4031 Log: - use nuiton-profiling to statistics call instead of Trace class - add method on StrategieMonthInfo to get all Metier with proportion Removed: trunk/src/main/java/fr/ifremer/isisfish/util/Trace.java Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java trunk/src/main/java/fr/ifremer/isisfish/entities/StrategyMonthInfoImpl.java trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java trunk/src/main/xmi/isis-fish.zargo Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/pom.xml 2014-07-08 17:24:51 UTC (rev 4031) @@ -79,6 +79,13 @@ </dependency> <dependency> + <groupId>org.nuiton</groupId> + <artifactId>nuiton-profiling</artifactId> + <version>2.7.2-SNAPSHOT</version> + <scope>compile</scope> + </dependency> + + <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> <version>2.4.2-SNAPSHOT</version> Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -35,7 +35,8 @@ import org.aspectj.lang.reflect.MethodSignature; import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.util.Trace; +import org.nuiton.profiling.Trace; +//import fr.ifremer.isisfish.util.Trace; /** * Permet de tracer les appels aux methodes utilisateur ainsi que l'execution @@ -79,9 +80,11 @@ + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " - + " || execution(* formules..*(..))") +// + " || execution(* formules..*(..))" + ) public void traceBeforeExecute(JoinPoint jp) { - getTrace().traceBefore(); + Method method = ((MethodSignature) jp.getSignature()).getMethod(); + getTrace().enter(method); } @AfterThrowing(throwing = "ex", @@ -89,7 +92,8 @@ + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " - + " || execution(* formules..*(..))") +// + " || execution(* formules..*(..))" + ) public void traceAfterThrowingExecute(JoinPoint jp, Exception ex) { // si une exeption est leve, il faut faire la meme chose traceAfterExecute(jp); @@ -99,9 +103,10 @@ + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " - + " || execution(* formules..*(..))") +// + " || execution(* formules..*(..))" + ) public void traceAfterExecute(JoinPoint jp) { Method method = ((MethodSignature) jp.getSignature()).getMethod(); - getTrace().traceAfterCall(method); + getTrace().exit(method); } } Modified: trunk/src/main/java/fr/ifremer/isisfish/entities/StrategyMonthInfoImpl.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/entities/StrategyMonthInfoImpl.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/entities/StrategyMonthInfoImpl.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -39,6 +39,7 @@ import fr.ifremer.isisfish.IsisFishRuntimeException; import fr.ifremer.isisfish.datastore.RegionStorage; import fr.ifremer.isisfish.datastore.StorageException; +import org.nuiton.math.matrix.MatrixIterator; /** * StrategyMonthInfoImpl. @@ -69,6 +70,16 @@ } } + @Override + public List<Metier> getMetierWithProportion() { + MatrixND mat = super.getProportionMetier(); + List<Metier> result = new ArrayList<Metier>(mat.getDim(0)); + for (MatrixIterator i=mat.iteratorNotZero(); i.next();) { + result.add((Metier)i.getSemanticsCoordinates()[0]); + } + return result; + } + public double getProportionMetier(Metier metier) { double result = 0; // on prend le super car ca ne sert a rien de mettre a jour, Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/SimulationContext.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -42,10 +42,11 @@ import fr.ifremer.isisfish.simulator.sensitivity.SensitivityUtils; import fr.ifremer.isisfish.types.TimeStep; import fr.ifremer.isisfish.util.IsisCache; -import fr.ifremer.isisfish.util.Trace; +//import fr.ifremer.isisfish.util.Trace; import org.nuiton.config.ApplicationConfig; import org.nuiton.config.OverwriteApplicationConfig; import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.profiling.Trace; /** * Keep all information on one simulation. @@ -140,7 +141,7 @@ SimulationContext current = get(); current.getCache().clear(); current.cache = null; - current.getTrace().clear(); + current.getTrace().clearStatistics(); current.trace = null; current.values.clear(); current.classLoader = null; @@ -248,7 +249,7 @@ public Trace getTrace() { if (trace == null) { - trace = new Trace(); + trace = new Trace(false, false); } return trace; } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -511,7 +511,7 @@ (end - start) / 1000000, "s'.'S")); SimulationParameter param = simulation.getParameter(); if (param.getUseStatistic()) { - String trace = context.getTrace().printStatisticAndClear(); + String trace = context.getTrace().getStatisticsCSV(); simulation.getInformation().setStatistic(trace); } if (param.getUseCache()) { Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCache.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -74,16 +74,16 @@ this.cacheBackend = cacheBackend; } - /** - * Return trace object from context. - * - * @return trace object from context - */ - protected Trace getTrace() { - SimulationContext context = SimulationContext.get(); - Trace result = context.getTrace(); - return result; - } +// /** +// * Return trace object from context. +// * +// * @return trace object from context +// */ +// protected org.nuiton.profiling.Trace getTrace() { +// SimulationContext context = SimulationContext.get(); +// org.nuiton.profiling.Trace result = context.getTrace(); +// return result; +// } /** * Recupere pour un pas de temps donnes une valeur calcule pour une cle. Modified: trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/util/IsisCacheBackendOnReferenceMap.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -84,16 +84,16 @@ 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; - } +// /** +// * 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; Deleted: trunk/src/main/java/fr/ifremer/isisfish/util/Trace.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/Trace.java 2014-07-07 16:53:07 UTC (rev 4030) +++ trunk/src/main/java/fr/ifremer/isisfish/util/Trace.java 2014-07-08 17:24:51 UTC (rev 4031) @@ -1,213 +0,0 @@ -/* - * #%L - * IsisFish - * - * $Id$ - * $HeadURL$ - * %% - * Copyright (C) 2002 - 2010 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 java.util.LinkedHashMap; -import java.util.Map; -import java.util.Stack; -import org.apache.commons.lang3.time.DurationFormatUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -/** - * Permet de tracer les appels aux methodes utilisateur ainsi que l'execution - * a ces methodes. La difference entre les deux est lors de l'utilisation du - * cache les appels seront superieur a l'execution car certaine valeur seront - * reutilisé dans le cache. - * - * @author poussin - * @version $Revision$ - * - * Last update: $Date$ - * by : $Author$ - */ -public class Trace { - - /** to use log facility, just put in your code: log.info(\"...\"); */ - static private Log log = LogFactory.getLog(Trace.class); - - /** nombre d'appel Cache inclus*/ - final static public int STAT_CALL = 0; - /** nombre d'appel reel qui a fait le calcul*/ - final static public int STAT_COMPUTATION = 1; - /** nombre d'appel vers une autre e depuis cette methode */ - final static public int STAT_CALL_NEST_METHOD = 2; - /** temps mini d'execution de cette methode (sans le temps des autres methodes) */ - final static public int STAT_TIME_MIN = 3; - /** temps max d'execution de cette methode (sans le temps des autres methodes) */ - final static public int STAT_TIME_MAX = 4; - /** temps total d'execution de cette methode (sans le temps des autres methodes) */ - final static public int STAT_TIME_TOTAL = 5; - /** temps total d'execution de cette methode (avec le temps des autres methodes) */ - final static public int STAT_TIME_TOTAL_NEST_METHOD = 6; - - /** nombre d'appel vers une autre e depuis cette methode */ - final static private int STACK_CALL_NEST_METHOD = 0; - /** heure de depart de l'appel a la methode (sans le temps des autres methodes) */ - final static private int STACK_TIME_START = 1; - /** heure de depart de l'appel a la methode (avec le temps des autres methodes) */ - final static private int STACK_TIME_START_NEST_METHOD = 2; - - /** array : [call's numbers, call do, min time, max time, total time, total time with child]*/ - protected Map<String, long[]> statistics = new LinkedHashMap<String, long[]>(); - - /** array : [nest e call, start time, start time with child] */ - protected Stack<long[]> callStack = new Stack<long[]>(); - - public Trace() { - } - - public long[] getStatistics(Object e) { - String key = String.valueOf(e); - long [] result = statistics.get(key); - if (result == null) { - result = new long[]{0, 0, 0, 0, 0, 0, 0}; - statistics.put(key, result); - } - return result; - } - - /** - * Clear current value statistics (all is reset) - */ - public void clear() { - statistics.clear(); - } - - public void traceBefore () { - // ajout dans le stack - long current = System.nanoTime(); - long [] stackItem = new long[]{0, current, current}; - callStack.push(stackItem); - } - - public void traceAfterCall(Object e) { - traceAfter(e, false); - } - public void traceAfterComputation(Object e) { - traceAfter(e, true); - } - - protected void traceAfter(Object e, boolean computation) { - long current = System.nanoTime(); - - if (callStack.isEmpty()) { - log.warn("Empty stack in after for " + e); - } else { - long [] stackItem = callStack.pop(); - long timeSpent = current - stackItem[STACK_TIME_START]; - long timeSpentNestMethod = current - stackItem[STACK_TIME_START_NEST_METHOD]; - - long [] stat = getStatistics(e); - if (computation) { - stat[STAT_COMPUTATION]++; // add +1 to computation number - } else { - // on incremente pas tout le temps STAT_CALL, car le plus - // souvent lors de l'utilisation de l'objet Trace dans un cache - // on a deja compte l'appel et reappelle lui meme computation - // ce qui ferait 2 appel alors qu'il n'y en a qu'un en realite - stat[STAT_CALL]++; // add +1 to call number - } - stat[STAT_CALL_NEST_METHOD] += stackItem[STACK_CALL_NEST_METHOD]; - stat[STAT_TIME_TOTAL] += timeSpent; - stat[STAT_TIME_TOTAL_NEST_METHOD] += timeSpentNestMethod; - if (stat[STAT_TIME_MIN] > timeSpent) { - stat[STAT_TIME_MIN] = timeSpent; - } - if (stat[STAT_TIME_MAX] < timeSpent) { - stat[STAT_TIME_MAX] = timeSpent; - } - - if (!callStack.isEmpty()) { - long [] parent = callStack.peek(); - parent[STACK_CALL_NEST_METHOD]++; // add +1 to call number nest e - parent[STACK_TIME_START] += timeSpentNestMethod; // remove to time all time spent in nest e (yes + to remove :) - } - } - - // ajouter le delta de temps dans le temps passé dans la méthod - - // il faud garder le temps passé dans l'appel d'autre methode de la stack - // --> A - // ========= - // --> B - // <-- B - // ========= - // --> C - // --> D - // <-- D - // <-- C - // ========= - // <-- A - - // le temps reellement passé dans A est representé par les ===== - } - - public String printStatisticAndClear() { - long call = 0; - long computation = 0; - StringBuffer result = new StringBuffer(); - result.append("--- " + " Statistics ---\n"); - for (String e : statistics.keySet()) { - long[] stat = getStatistics(e); - - // fix / by zero - // if Cache aspect has not been selected - if (stat[STAT_COMPUTATION] == 0) { - stat[STAT_COMPUTATION] = stat[STAT_CALL]; - } - - long meanTime = stat[STAT_TIME_TOTAL] / stat[STAT_COMPUTATION]; - call += stat[STAT_CALL]; - computation += stat[STAT_COMPUTATION]; - result.append( - e + - " call: " + stat[STAT_CALL] + - " computation: " + stat[STAT_COMPUTATION] + - // usage du cache - "(" + (100*stat[STAT_COMPUTATION]/stat[STAT_CALL]) + "%)" + - // Time is in nano not millis, we must divide by 1000000 - " min: " + DurationFormatUtils.formatDuration(stat[STAT_TIME_MIN] / 1000000, "s'.'S") + - " mean: " + DurationFormatUtils.formatDuration(meanTime / 1000000, "s'.'S") + - " max: " + DurationFormatUtils.formatDuration(stat[STAT_TIME_MAX] / 1000000, "s'.'S") + - " total: " + DurationFormatUtils.formatDuration(stat[STAT_TIME_TOTAL] / 1000000, "s'.'S") + - " call_nest: " + stat[STAT_CALL_NEST_METHOD] + - " total_with_nest: " + DurationFormatUtils.formatDuration(stat[STAT_TIME_TOTAL_NEST_METHOD] / 1000000, "s'.'S") + - "\n"); - } - result.append("--------------------\n"); - result.append("Total call: " + call + "\n"); - result.append("Total computation: " + computation + "\n"); - result.append("Cache usage: " + (100 * (call-computation) / (call+1/*+1 pour la / par 0 */) ) + "%" + "\n"); - result.append("--------------------\n"); - callStack.clear(); - statistics.clear(); - - System.out.println(result.toString()); - return result.toString(); - } - -} Modified: trunk/src/main/xmi/isis-fish.zargo =================================================================== (Binary files differ)

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r4030 - in trunk/src/main/java/fr/ifremer/isisfish: . aspect datastore simulator ui/input/check
by bpoussin＠users.forge.codelutin.com July 7, 2014

July 7, 2014

Author: bpoussin Date: 2014-07-07 18:53:07 +0200 (Mon, 07 Jul 2014) New Revision: 4030 Url: http://forge.codelutin.com/projects/isis-fish/repository/revisions/4030 Log: use new sparse matrix use new IteratorNotZero when possible Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java trunk/src/main/java/fr/ifremer/isisfish/ui/input/check/CheckRegion.java Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-01 15:33:08 UTC (rev 4029) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2014-07-07 16:53:07 UTC (rev 4030) @@ -54,7 +54,6 @@ import fr.ifremer.isisfish.actions.OtherAction; import fr.ifremer.isisfish.actions.SimulationAction; import fr.ifremer.isisfish.actions.VCSAction; -import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.simulator.SimulationContext; import fr.ifremer.isisfish.simulator.SimulationControl; import fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher; @@ -64,8 +63,7 @@ import fr.ifremer.isisfish.util.IsisCacheBackend; import fr.ifremer.isisfish.util.IsisCacheBackendOnGuava; import fr.ifremer.isisfish.vcs.VCS; -import org.nuiton.config.OverwriteApplicationConfig; -import org.nuiton.math.matrix.DoubleVector; +import org.nuiton.math.matrix.DoubleSparseHashVector; /** * Isis fish configuration. @@ -1083,7 +1081,7 @@ // pour les simulations SIMULATION_MATRIX_VECTOR_CLASS("simulation.matrix.vector.class", n("isisfish.config.simulation.matrix.vector.class.description"), DoubleBigVector.class.getName()), - SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleVector.class.getName()), + SIMULATION_MATRIX_VECTOR_SPARSE_CLASS("simulation.matrix.vector.sparse.class", n("isisfish.config.simulation.matrix.vector.sparse.class.description"), DoubleSparseHashVector.class.getName()), SIMULATION_MATRIX_THRESHOLD_USE_SPARSE_CLASS("simulation.matrix.threshold.use.sparse.class", n("isisfish.config.simulation.matrix.threshold.use.sparse.class.description"), "1000"), SIMULATION_STORE_RESULT_ON_DISK("simulation.store.result.ondisk", n("isisfish.config.simulation.store.result.ondisk.description"), "-1"), SIMULATION_STORE_RESULT_CACHE_STEP("simulation.store.result.cachestep", n("isisfish.config.simulation.store.result.cachestep.description"), "13"), Modified: trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-07-01 15:33:08 UTC (rev 4029) +++ trunk/src/main/java/fr/ifremer/isisfish/aspect/TraceAspect.java 2014-07-07 16:53:07 UTC (rev 4030) @@ -76,8 +76,6 @@ } @Before("execution(* scripts..*(..))" - + " || execution(* fr.ifremer.isisfish.entities..*(..))" - + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " @@ -88,8 +86,6 @@ @AfterThrowing(throwing = "ex", pointcut = "execution(* scripts..*(..))" - + " || execution(* fr.ifremer.isisfish.entities..*(..))" - + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " @@ -100,8 +96,6 @@ } @After("execution(* scripts..*(..))" - + " || execution(* fr.ifremer.isisfish.entities..*(..))" - + " || execution(* org.nuiton.math.matrix..*(..))" + " || execution(* simulators..*(..))" + " || execution(* rules..*(..)) " + " || execution(* simulationplans..*(..)) " Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2014-07-01 15:33:08 UTC (rev 4029) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2014-07-07 16:53:07 UTC (rev 4030) @@ -761,7 +761,7 @@ // mettre la matrice MatrixND submat = resultMat.getSubMatrix(0, d, 1); // on met les valeur de mat dans la sous matrice extraite - for (MatrixIterator mi = mat.iterator(); mi.next();) { + for (MatrixIterator mi = mat.iteratorNotZero(); mi.next();) { submat.setValue( ArrayUtil.concat(new Object[] { d }, mi.getSemanticsCoordinates()), mi.getValue()); Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java 2014-07-01 15:33:08 UTC (rev 4029) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/PopulationMonitor.java 2014-07-07 16:53:07 UTC (rev 4030) @@ -138,7 +138,7 @@ MatrixND n = getN(pop); if (n != null) { n = n.sumOverDim(1); - for (MatrixIterator i = n.iterator(); i.next();) { + for (MatrixIterator i = n.iteratorNotZero(); i.next();) { Object[] coord = i.getSemanticsCoordinates(); PopulationGroup group = (PopulationGroup) coord[0]; result += i.getValue() * group.getMeanWeight(); @@ -204,7 +204,7 @@ log.trace("Matrix repro before mortality: " + reproduction); } - for (MatrixIterator mi = reproduction.iterator(); mi.next();) { + for (MatrixIterator mi = reproduction.iteratorNotZero(); mi.next();) { Object[] sems = mi.getSemanticsCoordinates(); Zone z = (Zone) sems[0]; double coeff = pop.getNaturalDeathBirth(z); @@ -343,7 +343,7 @@ for (MatrixIterator i = catchPerStrategyMet.iterator(); i.next();) { this.totalHoldCatch += i.getValue(); } - + // this.totalHoldCatch += catchPerStrategyMet.sumAll(); } /** Modified: trunk/src/main/java/fr/ifremer/isisfish/ui/input/check/CheckRegion.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/ui/input/check/CheckRegion.java 2014-07-01 15:33:08 UTC (rev 4029) +++ trunk/src/main/java/fr/ifremer/isisfish/ui/input/check/CheckRegion.java 2014-07-07 16:53:07 UTC (rev 4030) @@ -168,8 +168,8 @@ static public boolean isNullMatrix(MatrixND mat) { boolean result = true; if (mat != null) { - for (MatrixIterator i = mat.iterator(); result && i.next();) { - result = i.getValue() == 0; + for (MatrixIterator i = mat.iteratorNotZero(); result && i.next();) { + result = false; } } return result; @@ -184,10 +184,7 @@ } static public double sumMatrix(MatrixND mat) { - double result = 0; - for (MatrixIterator i = mat.iterator(); i.next();) { - result += i.getValue(); - } + double result = mat.sumAll(); return result; }

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