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r3781 - trunk
by maven-release＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: maven-release Date: 2012-09-14 15:55:29 +0200 (Fri, 14 Sep 2012) New Revision: 3781 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3781 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-14 13:55:22 UTC (rev 3780) +++ trunk/pom.xml 2012-09-14 13:55:29 UTC (rev 3781) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.0.0</version> + <version>4.2.0.1-SNAPSHOT</version>  <dependencies> @@ -730,9 +730,9 @@   <scm> - <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</connection> - <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</developerConnection> - <url>http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</url> + <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</connection> + <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</developerConnection> + <url>http://svn.forge.codelutin.com/svn/isis-fish/trunk</url> </scm> <repositories>

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r3780 - in tags: . isis-fish-4.2.0.0
by maven-release＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: maven-release Date: 2012-09-14 15:55:22 +0200 (Fri, 14 Sep 2012) New Revision: 3780 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3780 Log: [maven-release-plugin] copy for tag isis-fish-4.2.0.0 Added: tags/isis-fish-4.2.0.0/ Property changes on: tags/isis-fish-4.2.0.0 ___________________________________________________________________ Added: svn:ignore + maven.log target velocity.log .classpath .project isis-fish.ipr isis-fish.iws isis-fish.iml .settings bin nbproject Inputs_Langoustine Added: svn:mergeinfo + /branches/4.1:3601-3670

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r3779 - trunk
by maven-release＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: maven-release Date: 2012-09-14 15:55:14 +0200 (Fri, 14 Sep 2012) New Revision: 3779 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3779 Log: [maven-release-plugin] prepare release isis-fish-4.2.0.0 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-14 13:50:15 UTC (rev 3778) +++ trunk/pom.xml 2012-09-14 13:55:14 UTC (rev 3779) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.2.0.0-SNAPSHOT</version> + <version>4.2.0.0</version>  <dependencies> @@ -730,9 +730,9 @@   <scm> - <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</connection> - <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/trunk</developerConnection> - <url>http://svn.forge.codelutin.com/svn/isis-fish/trunk</url> + <connection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</connection> + <developerConnection>scm:svn:http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</developerConnection> + <url>http://svn.forge.codelutin.com/svn/isis-fish/tags/isis-fish-4.2.0.0</url> </scm> <repositories>

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r3778 - in trunk/src: main/java/fr/ifremer/isisfish/util test/java/fr/ifremer/isisfish/util
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 15:50:15 +0200 (Fri, 14 Sep 2012) New Revision: 3778 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3778 Log: Add header Modified: trunk/src/main/java/fr/ifremer/isisfish/util/BitUtil.java trunk/src/test/java/fr/ifremer/isisfish/util/BitUtilTest.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/BitUtil.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/BitUtil.java 2012-09-14 13:46:18 UTC (rev 3777) +++ trunk/src/main/java/fr/ifremer/isisfish/util/BitUtil.java 2012-09-14 13:50:15 UTC (rev 3778) @@ -1,9 +1,31 @@ +/* + * #%L + * IsisFish + * + * $Id: BitUtil.java 3671 2012-04-03 13:31:36Z echatellier $ + * $HeadURL$ + * %% + * Copyright (C) 2012 Ifremer, 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 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ + package fr.ifremer.isisfish.util; - import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; /** * Quelques methodes pour manipuler les bits d'un long. Ces methodes servent pour @@ -17,8 +39,6 @@ */ public class BitUtil { - /** to use log facility, just put in your code: log.info(\"...\"); */ - static private Log log = LogFactory.getLog(BitUtil.class); /** * Converti une chaine de maximum 8 carateres en un long representant cette * chaine en ascii. Modified: trunk/src/test/java/fr/ifremer/isisfish/util/BitUtilTest.java =================================================================== --- trunk/src/test/java/fr/ifremer/isisfish/util/BitUtilTest.java 2012-09-14 13:46:18 UTC (rev 3777) +++ trunk/src/test/java/fr/ifremer/isisfish/util/BitUtilTest.java 2012-09-14 13:50:15 UTC (rev 3778) @@ -1,8 +1,30 @@ +/* + * #%L + * IsisFish + * + * $Id: BitUtil.java 3671 2012-04-03 13:31:36Z echatellier $ + * $HeadURL$ + * %% + * Copyright (C) 2012 Ifremer, 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 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ + package fr.ifremer.isisfish.util; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.junit.Assert; import org.junit.Test; @@ -16,8 +38,6 @@ */ public class BitUtilTest { - /** to use log facility, just put in your code: log.info(\"...\"); */ - static private Log log = LogFactory.getLog(BitUtilTest.class); /** * Test que la conversion chaine vers long fonctionne pour la creation de mark */

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r3777 - trunk
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 15:46:18 +0200 (Fri, 14 Sep 2012) New Revision: 3777 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3777 Log: Update to nuiton-matrix 2.3.2 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-14 08:59:15 UTC (rev 3776) +++ trunk/pom.xml 2012-09-14 13:46:18 UTC (rev 3777) @@ -62,14 +62,14 @@ <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix</artifactId> - <version>2.3.2-SNAPSHOT</version> + <version>2.3.2</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton.matrix</groupId> <artifactId>nuiton-matrix-gui</artifactId> - <version>2.3.2-SNAPSHOT</version> + <version>2.3.2</version> <scope>compile</scope> </dependency>

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r3776 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 10:59:15 +0200 (Fri, 14 Sep 2012) New Revision: 3776 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3776 Log: Prepare next version Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-09-14 08:56:58 UTC (rev 3775) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/SimulationStorage.java 2012-09-14 08:59:15 UTC (rev 3776) @@ -453,16 +453,16 @@ public ResultStorage getResultStorage() throws StorageException { if (resultStorage == null) { - // depuis la version 4.1.1.2 le stockage a changé de base + // depuis la version 4.2.0.0 le stockage a changé de base // de données à fichier mappe pour les resultat // mais il faut pouvoir relire les anciennes simulations SimulationParameter param = getParameter(); String isisFishVersion = param.getIsisFishVersion(); Version simuVersion = new Version(isisFishVersion); - Version version4112 = new Version(4,1,1,2); + Version version4200 = new Version(4, 2, 0, 0); // instancier un ResultStorage ou un ResultMappedStorage - if (simuVersion.before(version4112)) { + if (simuVersion.before(version4200)) { resultStorage = new ResultDatabaseStorage(this); } else { try {

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r3775 - in trunk: . src/main/java/fr/ifremer/isisfish
by echatellier＠users.forge.codelutin.com Sept. 14, 2012

Sept. 14, 2012

Author: echatellier Date: 2012-09-14 10:56:58 +0200 (Fri, 14 Sep 2012) New Revision: 3775 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3775 Log: Prepare next version Modified: trunk/pom.xml trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-09-11 18:06:45 UTC (rev 3774) +++ trunk/pom.xml 2012-09-14 08:56:58 UTC (rev 3775) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.1.1.2-SNAPSHOT</version> + <version>4.2.0.0-SNAPSHOT</version>  <dependencies> Modified: trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-09-11 18:06:45 UTC (rev 3774) +++ trunk/src/main/java/fr/ifremer/isisfish/IsisConfig.java 2012-09-14 08:56:58 UTC (rev 3775) @@ -119,7 +119,7 @@ * migration de donnees demande automatiquement un changement de version * d'application. */ - protected final static Version version = new Version(4, 1, 1, 2); + protected final static Version version = new Version(4, 2, 0, 0); protected final static Version majorVersion = new Version(version.getNumber(0)); protected final static Version databaseVersion = new Version(

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r3774 - trunk/src/main/java/fr/ifremer/isisfish/datastore
by bpoussin＠users.forge.codelutin.com Sept. 11, 2012

Sept. 11, 2012

Author: bpoussin Date: 2012-09-11 20:06:45 +0200 (Tue, 11 Sep 2012) New Revision: 3774 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3774 Log: utilisation de la representation interne de la chaine comme cle pour minimiser le nombre de chaine dans la JVM Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-09-11 17:56:00 UTC (rev 3773) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-09-11 18:06:45 UTC (rev 3774) @@ -129,6 +129,11 @@ if (result == null && internalValue != null) { result = internalValue; if (internalValue instanceof String) { + // on retrouve souvent les memes semantiques dans les matrices + // pour minimiser les chaines en memoire, on prend la representation + // interne avant de l'utiliser comme cle. + internalValue = ((String)internalValue).intern(); + result = internalValue; if (StringUtils.startsWith((String)internalValue, Month.class.getName())) { String val = StringUtils.substringAfter((String)internalValue, SEP); int monthNumber = Integer.parseInt(val); @@ -172,7 +177,10 @@ } else { result = String.valueOf(decoratedValue); } - cache.put(result, decoratedValue); + // on retrouve souvent les memes semantiques dans les matrices + // pour minimiser les chaines en memoire, on prend la representation + // interne avant de l'utiliser comme cle. + cache.put(((String)result).intern(), decoratedValue); } return result; } @@ -235,6 +243,9 @@ /** * Lit le header si possible. Si ce n'est pas possible replace le * raf a l'emplacement auquel il etait avant la tentative de lecture. + * + * Utilise pour toutes les chaines lu, la representation interne + * pour minimiser le nombre de chaine reellement en memoire * * @param raf * @return @@ -251,11 +262,11 @@ } else { result = new ResultHeaderMatrix(); result.stepValue = raf.readInt(); - result.name = raf.readUTF(); + result.name = raf.readUTF().intern(); result.dimSize = raf.readInt(); result.dimNames = new String[result.dimSize]; for (int i=0; i< result.dimSize; i++) { - result.dimNames[i] = raf.readUTF(); + result.dimNames[i] = raf.readUTF().intern(); } result.dims = new int[result.dimSize]; for (int i=0; i< result.dimSize; i++) { @@ -266,7 +277,7 @@ for (int i=0; i< result.dimSize; i++) { result.sems[i] = new ArrayList(); for (int j=0; j< result.dims[i]; j++) { - String s = raf.readUTF(); + String s = raf.readUTF().intern(); result.sems[i].add(s); } }

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r3773 - trunk/src/main/java/fr/ifremer/isisfish/util
by bpoussin＠users.forge.codelutin.com Sept. 11, 2012

Sept. 11, 2012

Author: bpoussin Date: 2012-09-11 19:56:00 +0200 (Tue, 11 Sep 2012) New Revision: 3773 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3773 Log: utilisation de la representation interne de la chaine comme cle pour minimiser le nombre de chaine dans la JVM Modified: trunk/src/main/java/fr/ifremer/isisfish/util/Cache.java Modified: trunk/src/main/java/fr/ifremer/isisfish/util/Cache.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/util/Cache.java 2012-09-11 07:57:50 UTC (rev 3772) +++ trunk/src/main/java/fr/ifremer/isisfish/util/Cache.java 2012-09-11 17:56:00 UTC (rev 3773) @@ -115,7 +115,10 @@ // le pas de temps trouve dans les arguments TimeStep step = computeKey(sbKey, method, args); - Object key = sbKey.toString(); + // 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) {

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r3772 - in trunk/src/main/java/fr/ifremer/isisfish: datastore simulator/launcher
by echatellier＠users.forge.codelutin.com Sept. 11, 2012

Sept. 11, 2012

Author: echatellier Date: 2012-09-11 09:57:50 +0200 (Tue, 11 Sep 2012) New Revision: 3772 Url: http://forge.codelutin.com/repositories/revision/isis-fish/3772 Log: Support delete and close for both database and file result storages. Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2012-09-07 23:51:36 UTC (rev 3771) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultDatabaseStorage.java 2012-09-11 07:57:50 UTC (rev 3772) @@ -102,6 +102,38 @@ this.simulation = simulation; } + @Override + public void delete() { + TopiaContext tx = null; + boolean mustClose = false; + + try { + if (simulation == SimulationContext.get().getSimulationStorage()) { + tx = SimulationContext.get().getDbResult(); + } + + if (tx == null) { + // not in simulation, create transaction + tx = simulation.getStorage().beginTransaction(); + mustClose = true; + } + + tx.execute("DELETE " + Result.class.getName()); + if (mustClose) { + tx.closeContext(); + } + } catch (Exception ex) { + if (log.isErrorEnabled()) { + log.error("Can't delete results", ex); + } + } + } + + @Override + public void close() { + // do nothing, closed by simulation storage closing + } + protected void putInCache(TimeStep step, String name, MatrixND mat, TopiaContext context) { String key = step.getStep() + ":" + name; putInCache(key, mat, context); @@ -518,7 +550,7 @@ // echatellier 20120829 : vidage du cache hibernate // sinon on fait trop de lecture que la meme transaction // et le cache hibernate se remplit sans se vider - tx.clearCache(); + //tx.clearCache(); } } catch (Exception eee) { if (log.isWarnEnabled()) { @@ -604,7 +636,7 @@ // echatellier 20120829 : vidage du cache hibernate // sinon on fait trop de lecture que la meme transaction // et le cache hibernate se remplit sans se vider - tx.clearCache(); + //tx.clearCache(); } } catch (TopiaException eee) { if (log.isWarnEnabled()) { Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-09-07 23:51:36 UTC (rev 3771) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultMappedStorage.java 2012-09-11 07:57:50 UTC (rev 3772) @@ -56,6 +56,7 @@ import java.util.TreeMap; import org.apache.commons.collections.BidiMap; import org.apache.commons.collections.bidimap.DualHashBidiMap; +import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -421,7 +422,22 @@ super.finalize(); raf.close(); } + + @Override + public void delete() { + close(); + File file = SimulationStorage.getResultFile(simulation.getDirectory()); + file.delete(); + } + @Override + public void close() { + if (raf != null) { + IOUtils.closeQuietly(raf); + raf = null; + } + } + /** * Methode interne pour que les deux Map soit mise a jour en meme temps * C'est la seul methode qui permet d'ajouter des noms de result dans les Map Modified: trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-09-07 23:51:36 UTC (rev 3771) +++ trunk/src/main/java/fr/ifremer/isisfish/datastore/ResultStorage.java 2012-09-11 07:57:50 UTC (rev 3772) @@ -149,4 +149,21 @@ * @return last simulation date */ public TimeStep getLastStep(); + + /** + * Delete all result for this result storage. + * + * In case of sensitivity analysis, after export, result are no longer + * needed and can be deleted to save disk space. + * + * @since 4.1.1.2 + */ + public void delete(); + + /** + * Close result storage. + * + * @since 4.1.1.2 + */ + public void close(); } Modified: trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java =================================================================== --- trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-09-07 23:51:36 UTC (rev 3771) +++ trunk/src/main/java/fr/ifremer/isisfish/simulator/launcher/InProcessSimulatorLauncher.java 2012-09-11 07:57:50 UTC (rev 3772) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2002 - 2010 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2002 - 2012 Ifremer, Code Lutin, 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 @@ -56,6 +56,7 @@ import fr.ifremer.isisfish.aspect.CacheAspect; import fr.ifremer.isisfish.aspect.RuleAspect; import fr.ifremer.isisfish.aspect.TraceAspect; +import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.datastore.SimulationStorage; import fr.ifremer.isisfish.datastore.SimulatorStorage; import fr.ifremer.isisfish.simulator.SimulationContext; @@ -66,8 +67,8 @@ import fr.ifremer.isisfish.simulator.SimulationParameter; import fr.ifremer.isisfish.simulator.SimulationPreScript; import fr.ifremer.isisfish.simulator.Simulator; +import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; /** * Fait une simulation dans la meme jvm. @@ -420,9 +421,11 @@ // suppression des résultats si l'utilisateur a demande à ne conserver // que les resultats de seulement la première simulation d'une AS + ResultStorage resultStorage = simulation.getResultStorage(); if (parameters.isSensitivityAnalysisOnlyKeepFirst() && !control.getId().endsWith("_0")) { - context.getDbResult().clear(true); + resultStorage.delete(); } + resultStorage.close(); } catch (OutOfMemoryError eee) { log.error(_("isisfish.error.during.simulation"), eee); @@ -437,14 +440,13 @@ // // Finaly close all TopiaContext used during simulation // - SimulationContext context = SimulationContext.get(); context.closeDB(); context.closeDBResult(); try { - // close all transaction + // close all transaction (root context) if (context.getSimulationStorage() != null) { context.getSimulationStorage().closeMemStorage(); context.getSimulationStorage().closeStorage();

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