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[ANN] - IsisFish 4.2.0.1 released
by forge.codelutin.com Release Notification Sept. 20, 2012

Sept. 20, 2012

The IsisFish team is pleased to announce the isis-fish-4.2.0.1 release! Simulateur de pecherie complexe. Documentation of the project can be found here: http://maven-site.forge.codelutin.com/isis-fish Changes ------- Changes in this version include: Fixed Bugs: o Impossible d'utiliser des appels R en sous process Issue: 1508. Thanks to Eric Chatellier. Resolved by echatellier. o Impossible de lire les resultats de simulation Issue: 1507. Thanks to Eric Chatellier. Resolved by echatellier. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/isis-fish/files * isis-fish-4.2.0.1-bin.zip - http://forge.codelutin.com/attachments/download/480 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -IsisFish team

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Pb de mémoire
by Paul MARCHAL Sept. 19, 2012

Sept. 19, 2012

Bonjour, J'ai voulu lancer 50 AS mais au bout de 10, Isis a levé le pouce. Il s'agit vraisemblablement d'un problème de mémoire. J'utilise la version 4.1.0.1. Je joins la fin du debug avec les messages d'erreur (trop gros pour être envoyé par mail en entier): ERROR [pool-4-thread-1] (JDBCExceptionReporter.java:234) logExceptions - Out of memory.; SQL statement: RUNSCRIPT FROM 'C:\Users\pmarchal\isis-fish-4\isis-database\simulations\as_deepv4_2012-09-13-19-09_29\data-backup.sql.gz' COMPRESSION GZIP [90108-166] ERROR [pool-4-thread-1] (InProcessSimulatorLauncher.java:148) simulate - Can't do simulation as_deepv4_2012-09-13-19-09_29 org.nuiton.topia.TopiaException: topia.persistence.error.on.restore at org.nuiton.topia.framework.TopiaContextImpl.restore(TopiaContextImpl.java:1349) at fr.ifremer.isisfish.datastore.SimulationStorage.importAndRenameZip(SimulationStorage.java:703) at fr.ifremer.isisfish.datastore.SimulationStorage.importAndRenameZip(SimulationStorage.java:653) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.simulate(InProcessSimulatorLauncher.java:123) at fr.ifremer.isisfish.simulator.launcher.SimulationJob.run(SimulationJob.java:287) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: org.hibernate.exception.GenericJDBCException: could not execute native bulk manipulation query at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140) at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:219) at org.hibernate.impl.SessionImpl.executeNativeUpdate(SessionImpl.java:1310) at org.hibernate.impl.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:396) at org.nuiton.topia.framework.TopiaContextImpl.restore(TopiaContextImpl.java:1344) ... 7 more Caused by: org.h2.jdbc.JdbcSQLException: Out of memory.; SQL statement: RUNSCRIPT FROM 'C:\Users\pmarchal\isis-fish-4\isis-database\simulations\as_deepv4_2012-09-13-19-09_29\data-backup.sql.gz' COMPRESSION GZIP [90108-166] at org.h2.message.DbException.getJdbcSQLException(DbException.java:329) at org.h2.message.DbException.get(DbException.java:158) at org.h2.message.DbException.convert(DbException.java:275) at org.h2.command.Command.executeUpdate(Command.java:230) at org.h2.jdbc.JdbcPreparedStatement.executeUpdateInternal(JdbcPreparedStatement.java:143) at org.h2.jdbc.JdbcPreparedStatement.executeUpdate(JdbcPreparedStatement.java:129) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:210) ... 10 more Caused by: java.lang.OutOfMemoryError: PermGen space INFO [pool-4-thread-1] (SimulationJob.java:209) run - Start simulation: as_deepv4_2012-09-13-19-09_30 INFO [pool-4-thread-1] (SimulationMonitor.java:364) simulationStart - Saving simulation as_deepv4_2012-09-13-19-09_30 as started INFO [pool-4-thread-1] (InProcessSimulatorLauncher.java:102) simulate - simulate as_deepv4_2012-09-13-19-09_30 with file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip INFO [pool-4-thread-1] (SimulationStorage.java:687) importAndRenameZip - Import simulation file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip in directory C:\Users\pmarchal\isis-fish-4\isis-database\simulations and rename from ^.*?/(.*)$ to as_deepv4_2012-09-13-19-09_30/$1 INFO [pool-4-thread-1] (SimulationStorage.java:694) importAndRenameZip - Last entry was as_deepv4_2012-09-13-19-09_30/simulators/DefaultSimulator.java extract name as_deepv4_2012-09-13-19-09_30 INFO [pool-4-thread-1] (DataStorage.java:209) getStorage - Create new storage for as_deepv4_2012-09-13-19-09_30 ERROR [pool-4-thread-1] (JavassistLazyInitializer.java:165) getProxyFactory - Javassist Enhancement failed: fr.ifremer.isisfish.entities.PopulationSeasonInfoImpl java.lang.OutOfMemoryError: PermGen space INFO [SimThread as_deepv4_2012-09-13-19-09_30] (InProcessSimulatorLauncher.java:316) localSimulateSameThread - 14/09/12 09:16 Java version: 1.6.0_24-b07 Isis-fish version: 4.1.0.0 INFO [SimThread as_deepv4_2012-09-13-19-09_30] (InProcessSimulatorLauncher.java:291) changeClassLoader - Classloader used for simulation: fr.ifremer.isisfish.aspect.AspectClassLoader@e68945 [file:/C:/Users/pmarchal/isis-fish-4/isis-database/simulations/as_deepv4_2012-09-13-19-09_30/, file:/C:/Users/pmarchal/isis-fish-4/isis-build/as_deepv4_2012-09-13-19-09_30/] INFO [SimThread as_deepv4_2012-09-13-19-09_30] (InProcessSimulatorLauncher.java:203) message - Mise en place des aspects Cache INFO [SimThread as_deepv4_2012-09-13-19-09_30] (SimulationControl.java:202) setText - Mise en place des aspects Cache ERROR [SimThread as_deepv4_2012-09-13-19-09_30] (InProcessSimulatorLauncher.java:429) localSimulateSameThread - Error during simulation java.lang.OutOfMemoryError: PermGen space INFO [SimThread as_deepv4_2012-09-13-19-09_30] (InProcessSimulatorLauncher.java:463) localSimulateSameThread - Simulation time: 2.074 ERROR [SimThread as_deepv4_2012-09-13-19-09_30] (IsisFish.java:635) uncaughtException - Global application exception fr.ifremer.isisfish.simulator.SimulationException: Out of memory try with more memory (option -mx) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.localSimulateSameThread(InProcessSimulatorLauncher.java:431) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher$SimThread.run(InProcessSimulatorLauncher.java:265) Caused by: java.lang.OutOfMemoryError: PermGen space INFO [monitor-thread] (SimulationMonitor.java:477) waitAndCheckProgression - Job as_deepv4_2012-09-13-19-09_30 finished INFO [monitor-thread] (SimulationMonitor.java:590) doPostSimulationOperation - Do post simulation operation for as_deepv4_2012-09-13-19-09_30 INFO [monitor-thread] (SimulationControl.java:202) setText - Recherche de la dernière simulation INFO [monitor-thread] (SimulationControl.java:202) setText - Simulation terminée INFO [monitor-thread] (SimulationMonitor.java:408) simulationStop - Saving simulation as_deepv4_2012-09-13-19-09_30 as stopped INFO [pool-4-thread-1] (SimulationJob.java:209) run - Start simulation: as_deepv4_2012-09-13-19-09_31 INFO [pool-4-thread-1] (SimulationMonitor.java:364) simulationStart - Saving simulation as_deepv4_2012-09-13-19-09_31 as started INFO [pool-4-thread-1] (InProcessSimulatorLauncher.java:102) simulate - simulate as_deepv4_2012-09-13-19-09_31 with file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip INFO [pool-4-thread-1] (SimulationStorage.java:687) importAndRenameZip - Import simulation file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip in directory C:\Users\pmarchal\isis-fish-4\isis-database\simulations and rename from ^.*?/(.*)$ to as_deepv4_2012-09-13-19-09_31/$1 INFO [pool-4-thread-1] (SimulationStorage.java:694) importAndRenameZip - Last entry was as_deepv4_2012-09-13-19-09_31/simulators/DefaultSimulator.java extract name as_deepv4_2012-09-13-19-09_31 INFO [pool-4-thread-1] (DataStorage.java:209) getStorage - Create new storage for as_deepv4_2012-09-13-19-09_31 WARN [pool-4-thread-1] (SimulationJob.java:342) run - Can't simulate as_deepv4_2012-09-13-19-09_31 java.lang.OutOfMemoryError: PermGen space INFO [pool-4-thread-1] (SimulationJob.java:209) run - Start simulation: as_deepv4_2012-09-13-19-09_32 INFO [pool-4-thread-1] (SimulationMonitor.java:364) simulationStart - Saving simulation as_deepv4_2012-09-13-19-09_32 as started INFO [pool-4-thread-1] (InProcessSimulatorLauncher.java:102) simulate - simulate as_deepv4_2012-09-13-19-09_32 with file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip INFO [pool-4-thread-1] (SimulationStorage.java:687) importAndRenameZip - Import simulation file C:\Users\pmarchal\AppData\Local\Temp\isisfish-simulation-1347556173156-preparation.zip in directory C:\Users\pmarchal\isis-fish-4\isis-database\simulations and rename from ^.*?/(.*)$ to as_deepv4_2012-09-13-19-09_32/$1 INFO [pool-4-thread-1] (SimulationStorage.java:694) importAndRenameZip - Last entry was as_deepv4_2012-09-13-19-09_32/simulators/DefaultSimulator.java extract name as_deepv4_2012-09-13-19-09_32 INFO [pool-4-thread-1] (DataStorage.java:209) getStorage - Create new storage for as_deepv4_2012-09-13-19-09_32 ERROR [pool-4-thread-1] (JavassistLazyInitializer.java:165) getProxyFactory - Javassist Enhancement failed: fr.ifremer.isisfish.entities.PopulationSeasonInfoImpl java.lang.OutOfMemoryError: PermGen space INFO [SimThread as_deepv4_2012-09-13-19-09_32] (InProcessSimulatorLauncher.java:316) localSimulateSameThread - 14/09/12 09:16 Java version: 1.6.0_24-b07 Isis-fish version: 4.1.0.0 INFO [SimThread as_deepv4_2012-09-13-19-09_32] (InProcessSimulatorLauncher.java:291) changeClassLoader - Classloader used for simulation: fr.ifremer.isisfish.aspect.AspectClassLoader@858c86 [file:/C:/Users/pmarchal/isis-fish-4/isis-database/simulations/as_deepv4_2012-09-13-19-09_32/, file:/C:/Users/pmarchal/isis-fish-4/isis-build/as_deepv4_2012-09-13-19-09_32/] INFO [SimThread as_deepv4_2012-09-13-19-09_32] (InProcessSimulatorLauncher.java:203) message - Mise en place des aspects Cache INFO [SimThread as_deepv4_2012-09-13-19-09_32] (SimulationControl.java:202) setText - Mise en place des aspects Cache INFO [SimThread as_deepv4_2012-09-13-19-09_32] (DataStorage.java:164) getMemStorage - Create new memory storage for as_deepv4_2012-09-13-19-09_32 ERROR [SimThread as_deepv4_2012-09-13-19-09_32] (InProcessSimulatorLauncher.java:429) localSimulateSameThread - Error during simulation java.lang.OutOfMemoryError: PermGen space INFO [monitor-thread] (SimulationMonitor.java:477) waitAndCheckProgression - Job as_deepv4_2012-09-13-19-09_32 finished INFO [monitor-thread] (SimulationMonitor.java:590) doPostSimulationOperation - Do post simulation operation for as_deepv4_2012-09-13-19-09_32 INFO [monitor-thread] (SimulationControl.java:202) setText - Recherche de la dernière simulation INFO [monitor-thread] (SimulationControl.java:202) setText - Simulation terminée INFO [monitor-thread] (SimulationMonitor.java:408) simulationStop - Saving simulation as_deepv4_2012-09-13-19-09_32 as stopped INFO [SimThread as_deepv4_2012-09-13-19-09_32] (InProcessSimulatorLauncher.java:463) localSimulateSameThread - Simulation time: 2.167 ERROR [SimThread as_deepv4_2012-09-13-19-09_32] (IsisFish.java:635) uncaughtException - Global application exception fr.ifremer.isisfish.simulator.SimulationException: Out of memory try with more memory (option -mx) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher.localSimulateSameThread(InProcessSimulatorLauncher.java:431) at fr.ifremer.isisfish.simulator.launcher.InProcessSimulatorLauncher$SimThread.run(InProcessSimulatorLauncher.java:265) Caused by: java.lang.OutOfMemoryError: PermGen space Merci pour vos lumières Paul -- Paul Marchal IFREMER DOP/DHMMN Laboratoire Ressources Halieutiques de Boulogne/mer Boulogne/mer Fishery Resources Laboratory http://wwz.ifremer.fr/manchemerdunord 150, Quai Gambetta BP 699 62321 Boulogne sur mer FRANCE Tel: (+33) 321 99 56 86 Fax: (+33) 321 99 56 01 Mail: paul.marchal(a)ifremer.fr

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[ANN] - IsisFish 4.2.0.0 released
by forge.codelutin.com Release Notification Sept. 14, 2012

Sept. 14, 2012

The IsisFish team is pleased to announce the isis-fish-4.2.0.0 release! Simulateur de pecherie complexe. Documentation of the project can be found here: http://maven-site.forge.codelutin.com/isis-fish Changes ------- Changes in this version include: New features: o Add new result storage to store result on file system Issue: 1449. Thanks to Eric Chatellier. Resolved by echatellier. Fixed Bugs: o Le dépot communauté n'est pas mis à jour au démarrage Issue: 1461. Thanks to Eric Chatellier. Resolved by echatellier. o Impossible d'appeler R depuis un sous processus Issue: 1460. Thanks to Eric Chatellier. Resolved by echatellier. Downloads --------- For a manual installation, you can download files here: http://forge.codelutin.com/projects/isis-fish/files * isis-fish-4.2.0.0-bin.zip - http://forge.codelutin.com/attachments/download/472 Maven artifacts --------------- Artifacts are deployed in nuiton maven repository http://maven.nuiton.org/other-releases/ Have fun! -IsisFish team

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Nouveau format de stockage des résultats de simulations
by Eric Chatellier Sept. 14, 2012

Sept. 14, 2012

Bonjour, Nous avons développé un nouveau format de stockage des résultats commençant avec la version 4.2.0.0 de IsisFish. Ce nouveau format ne stock plus les résultats dans la base de données, mais dans un fichier indexé enregistré dans le dossier de la simulation. Ce nouveau format de stockage est plus rapide lors de l’exécution de la simulation et beaucoup plus rapide pendant la phase d'export des résultats (de l'ordre de six fois plus rapide). Il résous également un problème mémoire pendant la phase d'export. Concernant son utilisation, il n'y a aucune différence dans l'API. Ce nouveau stockage est une nouvelle implémentation du ResultManager et s'utilise exactement de la même façon que l'ancien. Cela ne change rien du point de vue de l'utilisateur. Cordialement, Eric Chatellier. -- Éric Chatellier <chatellier(a)codelutin.com> Tel: 02.40.50.29.28 http://www.codelutin.com

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script de pre-simulation
by Stephanie MAHEVAS Sept. 14, 2012

Sept. 14, 2012

Bonjour je voudrais faire un script de presimu qui me change les valeurs de capturabilité. voila le bout de script que j'ai prepare.Mais je ne sais pas comment acceder au simulationStorage et je ne sais pas si la forme/structure est correcte Quelqu'un peut-il jeter un oeil? merci Stephanie -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

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pb de lancement de simu avec nouveau disque dur
by Stephanie MAHEVAS Sept. 13, 2012

Sept. 13, 2012

Eric il semblerait que le lancement avec le disque dur externe ne marche pas... tu peux regarder? D'apres Olivier ca pourrait venir du format disque (NTFS-3G) merci steph -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

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script calibration
by Stephanie MAHEVAS Sept. 13, 2012

Sept. 13, 2012

je voudrais etre sure de ce que ce script fait... Quel partie de ma matrice L2.getSubMatrix(1,2,4).prend ce script???? sachant que les dimensions de L2 = MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP sont /** * Matrix with five dimensions * Dimension 1 : TimeStep * Dimension 2 : Strategy * Dimension 3 : Metier * Dimension 4 : Group * Dimension 5 : Zone */ bout de script dont c'est issu: MatrixND L2 = result.getMatrix(param_Population, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); // log.info("dim de L2" + " " + Arrays.toString(L2.getDim())); /////*** If some strategies, metiers or areas must not be included in the cumulated catches see below else put "//" at the beginning of line 297 and replace "L2" by "L" at line 289 /////*** the strategies or so to exclude must be at the begining or end of the list you enter in the parameters interface /////*** fill the line MatrixND L = L2.getSubMatrix(a,b,c).copy(); as follow : /////*** a = 1 if you want to exclude strategies, 2 if metiers and 4 if areas /////*** b = indice of the first object considered /////*** c = number of object to keep after b, b included MatrixND L = L2.getSubMatrix(1,2,4).copy(); Merci steph -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

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Re: [Isis-fish-users] Fwd: les simulations ne se rappatrient pas de caparmor
by Eric Chatellier Sept. 10, 2012

Sept. 10, 2012

Le 10/09/2012 13:42, Olivier BERTHELE a écrit : > Coucou, > > Voilà, Isis est relancé. > Il affiche qu'il est en train de télécharger les résultats... Ok merci. Je vais verifier l'algorithme de controle des simulations en cours pour voir pourquoi il s'arrete seulement pour caparmor. -- Éric Chatellier <chatellier(a)codelutin.com> Tel: 02.40.50.29.28 http://www.codelutin.com

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Fwd: les simulations ne se rappatrient pas de caparmor
by Stephanie.Mahevas＠ifremer.fr Sept. 10, 2012

Sept. 10, 2012

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plan de simu et caparmor
by Stephanie MAHEVAS Sept. 7, 2012

Sept. 7, 2012

Eric, il restent deux simulations de caparmor dans le haut de l'interface de la queue de simulation (simulation terminée). Il semblerait que ISIS n'arrive pas à les recuperer. Est-ce que je quitte ISIS et le relance? Les autres sont bel et bien finies et rappatriées pour celles de caparmor. IL n'y a pas photo entre les tps de simu sur Caparmor (15') et sur ceux le serveur (~4h mais surement polué par les dezippages) a+ steph -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

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