January 2017 - Isis-fish-users - mailman.cloud.codelutin.com

arret d'un plan d optimisation
by Sigrid Lehuta 30 Jan '17

30 Jan '17

hello, cette nuit mon plan s'est arreté a la 829e simu sur 4000. il a commencé par marquer "simu terminée" et à descendre la simu avec les terminées alors que la barre de progression est à 0 avec le log ci dessous, puis il a fait d autres simus marquée "terminée" avec la barre a 0, qu il n a pas descendues. le debug est bizarrement vide ... je precise qu isis avait courageusement realisé 2 ou 3 plans d optim (14000 simus) d afilé sans que je le ferme... peut etre qu il avait besoin de repos... merci WARN|21:06:22,726|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,727|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,727|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,728|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,728|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,728|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,729|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,735|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,735|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,736|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,737|ResultManager.java|202|addActiveRule|addActiveRule not implemented WARN|21:06:22,750|ResultManager.java|202|addActiveRule|addActiveRule not implemented INFO|21:06:22,751|SimulationControl.java|206|setText|Do pre action Rules INFO|21:06:24,375|SimulationControl.java|206|setText|Simulate one month ERROR|21:06:44,318|InProcessSimulatorLauncher.java|485|localSimulateSameThread|Error during simulation fr.ifremer.isisfish.IsisFishRuntimeException: Impossible d'Ã©valuer l'Ã©quation: return 1; at fr.ifremer.isisfish.entities.EquationImpl.evaluate(EquationImpl.java:90) ~[isis-fish-4.4.0.2.jar:?] at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source) ~[?:?] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_111] at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_111] at org.hibernate.proxy.pojo.javassist.JavassistLazyInitializer.invoke(JavassistLazyInitializer.java:196) ~[hibernate-core-4.3.11.Final.jar:4.3.11.Final] at fr.ifremer.isisfish.entities.EquationImpl_$$_jvst57e_6.evaluate(EquationImpl_$$_jvst57e_6.java) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.entities.SelectivityImpl.getCoefficient(SelectivityImpl.java:63) ~[isis-fish-4.4.0.2.jar:?] at scripts.SiMatrixEffortByCell.matrixFishingMortalityPerCell_aroundBody14(SiMatrixEffortByCell.java:330) ~[?:?] at scripts.SiMatrixEffortByCell$AjcClosure15.run(SiMatrixEffortByCell.java:1) ~[?:?] at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149) ~[aspectjweaver-1.8.8.jar:1.8.8] at fr.ifremer.isisfish.util.IsisCache.realCall(IsisCache.java:202) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.util.IsisCache.get(IsisCache.java:143) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.aspect.CacheAspect.call(CacheAspect.java:73) ~[?:?] at scripts.SiMatrixEffortByCell.matrixFishingMortalityPerCell(SiMatrixEffortByCell.java:280) ~[?:?]

2 2

problemes d'arrondis
by Sigrid Lehuta 27 Jan '17

27 Jan '17

Comme expliqué à Benjamin hier, java me fait des arrondis aléatoirement... Ici dans le meme plan d experience (optimisation) qui tourne sur 3pop en meme temps, il arrondit différemment selon la pop, il calcule la fonction objectif correctement pour cod mais fait des arrondis intempestifs pour plaice et whiting. par contre il est consistant pour une pop... je crois que ca vient de l utilisation de l ecriture scientifique des nombres ex. 2.5e7 qd il a recours a cette ecriture il supprime une bonne partie des chiffres après la virgule (idem pour les parametres en e-7) tandis que pour cod les valeurs sont plus faibles et ecrites entierement ex. 324653.002... les fo calculées pour chaque simus sont dans le fichier xlsx d'historique joint colonne "objective" je mets aussi une simu. Merci !

2 1

config R
by Sigrid Lehuta 21 Jan '17

21 Jan '17

Salut, en preparant le cours ISIS qu on donne lundi isis a été installé sur plusieurs PC a l'ecole. la connection avec R ne se fait pas. J'ai essayé chez moi pour voir et xca ne fonctionne pas non plus. voici ce que j ai fait : - verifié la version de java : 64 bits - creé la variable R_HOME C:\Program Files\R\R-3.2.5 - modifié la variable path : en ajoutant %R_HOME%\bin\x64 - installé rJava dans la version 3.2.5 de R La fenetre de config indique R_HOME : C:\Program Files\R\R-3.2.5 R.type : jni PATH : Le path ne contient pas le dossier bin de R (C:\Program Files\R\R-3.2.5\bin) Merci !

2 3

ISIS refuse de s'ouvrir suite à un changement du nom de repertoire
by smahevas 20 Jan '17

20 Jan '17

Bonjour ISIS refuse de s'ouvrir (V4.4.0.2) suite à un changement de nom de mon repertoire de travail (initialement ISISFish, devenu C-ISISFish. Je suis allée changer la configuration dans l'interface et il me met le message d'erreur suivant si quelqu'un a une idee... merci Stephanie INFO [main] (IsisFish.java:136) main - Starting Isis-Fish 4.4.0.2 with args : [] INFO [main] (IsisFish.java:137) main - Date: 16/01/17 10:59 INFO [main] (IsisFish.java:138) main - Java version: 1.8.0_71-b15, Java HotSpot(TM) Client VM INFO [main] (IsisFish.java:139) main - Plaform/arch: Windows 7/x86 INFO [main] (IsisFish.java:140) main - R_HOME: C:\Program Files\R\R-3.0.2 INFO [main] (IsisFish.java:141) main - PATH: C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Program Files\Dell\DW WLAN Card;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth Software\syswow64;C:\Program Files\Dell\Dell Data Protection\Access\Advanced\Wave\Gemalto\Access Client\v5\;C:\Program Files (x86)\Security Innovation\SI TSS\bin\;C:\Program Files (x86)\Graphviz 2.28\bin;C:\Program Files (x86)\QuickTime\QTSystem\;C:\Program Files (x86)\Skype\Phone\;C:\Program Files (x86)\GTK2-Runtime\bin;C:\Program Files\R\R-3.0.2\bin\i386;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\ INFO [main] (IsisFish.java:354) initVCS - Check state of local repository: C:\Users\smahevas\C-ISISFish\isis-fish-4\isis-database INFO [main] (VCSSVN.java:144) getSVNManager - Try to connect to http://svn.forge.codelutin.com/svn/isis-fish-data INFO [main] (VCSSVN.java:236) isConnected - Connexion au serveur disponible, passage en mode connecté : http://svn.forge.codelutin.com/svn/isis-fish-data WARN [main] (IsisFish.java:159) main - Error during vcs initialisation fr.ifremer.isisfish.vcs.VCSException: Impossible de déverrouiller la copie locale at fr.ifremer.isisfish.vcs.VCSSVN.cleanup(VCSSVN.java:412) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.IsisFish.initVCS(IsisFish.java:436) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.IsisFish.main(IsisFish.java:155) [isis-fish-4.4.0.2.jar:?] Caused by: org.tmatesoft.svn.core.SVNException: svn: E155021: Unsupported working copy format at org.tmatesoft.svn.core.internal.wc.SVNErrorManager.error(SVNErrorManager.java:64) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc.SVNErrorManager.error(SVNErrorManager.java:51) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc17.db.SVNWCDb.verifyDirUsable(SVNWCDb.java:4864) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc17.db.SVNWCDb.obtainWcRoot(SVNWCDb.java:6277) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc17.db.SVNWCDb.obtainWcRoot(SVNWCDb.java:6269) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc17.db.SVNWCDb.readInfo(SVNWCDb.java:3532) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.repairTimestamps(SvnNgCleanup.java:87) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.repairTimestamps(SvnNgCleanup.java:106) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.cleanupInternal(SvnNgCleanup.java:81) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.cleanup(SvnNgCleanup.java:47) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.run(SvnNgCleanup.java:38) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgCleanup.run(SvnNgCleanup.java:24) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.ng.SvnNgOperationRunner.run(SvnNgOperationRunner.java:20) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.internal.wc2.SvnOperationRunner.run(SvnOperationRunner.java:21) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.wc2.SvnOperationFactory.run(SvnOperationFactory.java:1235) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.wc2.SvnOperation.run(SvnOperation.java:294) ~[svnkit-1.8.11.jar:?] at org.tmatesoft.svn.core.wc.SVNWCClient.doCleanup(SVNWCClient.java:386) ~[svnkit-1.8.11.jar:?] at fr.ifremer.isisfish.vcs.VCSSVN.cleanup(VCSSVN.java:410) ~[isis-fish-4.4.0.2.jar:?] ... 2 more INFO [main] (IsisFish.java:166) main - after init done in 2.315. INFO [Thread-4] (CronService.java:84) run - Starting 1 registered services INFO [AWT-EventQueue-0] (SimulationExecutor.java:87) <init> - SimulationExecutor started with 8 thread for dans un sous processus INFO [AWT-EventQueue-0] (SimulationExecutor.java:87) <init> - SimulationExecutor started with 2 thread for sur le serveur Caparmor INFO [AWT-EventQueue-0] (SimulationExecutor.java:87) <init> - SimulationExecutor started with 2 thread for dans le même processus INFO [AWT-EventQueue-0] (IsisTray.java:117) getInstance - Use system tray: fr.ifremer.isisfish.IsisTray$AWTSystemTray ERROR [AWT-EventQueue-0] (IsisFish.java:685) uncaughtException - Global application exception java.lang.NullPointerException at fr.ifremer.isisfish.datastore.VersionStorage.getStorageNames(VersionStorage.java:404) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.datastore.RegionStorage.getRegionNames(RegionStorage.java:320) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.input.InputUI.$completeSetup(InputUI.java:666) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.input.InputUI.$initialize(InputUI.java:786) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.input.InputUI.<init>(InputUI.java:186) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeTabUI.createInputUI(WelcomeTabUI.java:374) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeTabUI.$initialize(WelcomeTabUI.java:429) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeTabUI.<init>(WelcomeTabUI.java:145) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeHandler.afterInit(WelcomeHandler.java:99) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeUI.$afterCompleteSetup(WelcomeUI.java:118) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeUI.$completeSetup(WelcomeUI.java:605) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeUI.$initialize(WelcomeUI.java:776) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.ui.WelcomeUI.<init>(WelcomeUI.java:142) ~[isis-fish-4.4.0.2.jar:?] at fr.ifremer.isisfish.IsisFish$3.run(IsisFish.java:719) ~[isis-fish-4.4.0.2.jar:?] at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:1.8.0_71] at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:1.8.0_71] at java.awt.EventQueue.access$500(Unknown Source) ~[?:1.8.0_71] at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_71] at java.awt.EventQueue$3.run(Unknown Source) ~[?:1.8.0_71] at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_71] at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:1.8.0_71] at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:1.8.0_71] at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_71] at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_71] at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_71] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_71] at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_71] at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_71] org.apache.commons.mail.EmailException: Sending the email to the following server failed : smtp:25 at org.apache.commons.mail.Email.sendMimeMessage(Email.java:1421) at org.apache.commons.mail.Email.send(Email.java:1448) at fr.ifremer.isisfish.ui.util.ErrorHelper.reportError(ErrorHelper.java:161) at org.jdesktop.swingx.plaf.basic.BasicErrorPaneUI$1.actionPerformed(BasicErrorPaneUI.java:197) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.WaitDispatchSupport$2.run(Unknown Source) at java.awt.WaitDispatchSupport$4.run(Unknown Source) at java.awt.WaitDispatchSupport$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.awt.WaitDispatchSupport.enter(Unknown Source) at java.awt.Dialog.show(Unknown Source) at java.awt.Component.show(Unknown Source) at java.awt.Component.setVisible(Unknown Source) at java.awt.Window.setVisible(Unknown Source) at java.awt.Dialog.setVisible(Unknown Source) at org.jdesktop.swingx.JXErrorPane$1.run(JXErrorPane.java:398) at org.jdesktop.swingx.JXErrorPane.showDialog(JXErrorPane.java:411) at fr.ifremer.isisfish.ui.util.ErrorHelper.showErrorDialog(ErrorHelper.java:81) at fr.ifremer.isisfish.IsisFish$3$1.uncaughtException(IsisFish.java:695) at java.lang.ThreadGroup.uncaughtException(Unknown Source) at java.lang.ThreadGroup.uncaughtException(Unknown Source) at java.awt.EventDispatchThread.processException(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: com.sun.mail.util.MailConnectException: Couldn't connect to host, port: smtp, 25; timeout 60000; nested exception is: java.net.ConnectException: Connection refused: connect at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2100) at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:699) at javax.mail.Service.connect(Service.java:366) at javax.mail.Service.connect(Service.java:246) at javax.mail.Service.connect(Service.java:195) at javax.mail.Transport.send0(Transport.java:254) at javax.mail.Transport.send(Transport.java:124) at org.apache.commons.mail.Email.sendMimeMessage(Email.java:1411) ... 59 more Caused by: java.net.ConnectException: Connection refused: connect at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) at java.net.AbstractPlainSocketImpl.connect(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.SocksSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:329) at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:238) at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2066) ... 66 more ^C

4 14

arrondis
by Sigrid Lehuta 17 Jan '17

17 Jan '17

Hello, puis je avoir confirmation que double obj = (sim - obs) /1000 ; me donne l'arrondi ? J'aurais dû faire (sim-obj) / 1000.0 pour garder les chiffres apres la virgule c'est ca ? Merci

2 1

Nouvelle regle Gravité base GdG demersal pour la V4.4
by Sigrid Lehuta 11 Jan '17

11 Jan '17

Hello la regle GraviteVPUE1LangEtGrossValueOtherSpeciesECOMOD écrite pour la base GdG demersal ne fonctionne pas telle quelle en V4.4 Voici la version corrigée.

1 0

optimization- exports
by Sigrid Lehuta 06 Jan '17

06 Jan '17

Hello je tente d utiliser les exports dans l interface d optimization pour calculer la fonction d objectif. je ne suis pas sure de la structure de ces objets... du coup ce n'est pas des matrices mais des csv dans lesquels les matrices ont été mises à plat c'est ca ? Du coup il faudrait faire pareil avec les observations et les rentrer comme des matrices à plat ? Peut on vraiment faire ca dans l interface observation ? les matrices créées ne prennent que des valeurs pas des strings ? et du coup comment s'assurer que les valeurs sont rangées dans le meme ordre ? J'avoue que je serai plus a l aise avec des matrices ayant des semantics meme s'il faut du coup aussi les construire pour les observations... Je pense qu il faudra en rediscuter. Merci de votre réponse

2 2