I precise, this error only happen with EGI environnement and not with LocalEnvironnement. And this error crash openmole in terminal.
2016-11-25 21:28 GMT+01:00 reyman <[email protected]>: > Uh thanks, but i have a weird error now : > > Picked up _JAVA_OPTIONS: -Xms1024m -Xmx2G -Xss256m > Nouvelle fenêtre ouverte dans la session du navigateur > nov. 25, 2016 9:23:45 PM org.openmole.ui.Application$$ > anonfun$run$1$$anonfun$apply$mcI$sp$6 apply > INFOS: Server listening on port 41947. > !SESSION 2016-11-25 21:24:28.668 ------------------------------ > ----------------- > eclipse.buildId=unknown > java.version=1.8.0_101 > java.vendor=Oracle Corporation > BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=fr_FR > > !ENTRY org.apache.commons.configuration2 4 0 2016-11-25 21:24:28.668 > !MESSAGE FrameworkEvent ERROR > !STACK 0 > java.io.IOException: Exception in opening zip file: > /home/reyman/.openmole/.tmp/1480105414_12098/org.eclipse.os > gi/90/0/bundleFile > at org.eclipse.osgi.framework.util.SecureAction.getZipFile( > SecureAction.java:305) > at org.eclipse.osgi.storage.bundlefile.ZipBundleFile. > basicOpen(ZipBundleFile.java:85) > at org.eclipse.osgi.storage.bundlefile.ZipBundleFile. > getZipFile(ZipBundleFile.java:98) > at org.eclipse.osgi.storage.bundlefile.ZipBundleFile. > checkedOpen(ZipBundleFile.java:65) > at org.eclipse.osgi.storage.bundlefile.ZipBundleFile. > getEntry(ZipBundleFile.java:232) > at org.eclipse.osgi.internal.loader.classpath.ClasspathManager. > findClassImpl(ClasspathManager.java:562) > at org.eclipse.osgi.internal.loader.classpath.ClasspathManager. > findLocalClassImpl(ClasspathManager.java > :540) > at org.eclipse.osgi.internal.loader.classpath.ClasspathManager. > findLocalClass(ClasspathManager.java:527 > ) > at org.eclipse.osgi.internal.loader.ModuleClassLoader. > findLocalClass(ModuleClassLoader.java:324) > at org.eclipse.osgi.internal.loader.BundleLoader. > findLocalClass(BundleLoader.java:311) > at org.eclipse.osgi.internal.loader.BundleLoader. > findClassInternal(BundleLoader.java:386) > at org.eclipse.osgi.internal.loader.BundleLoader.findClass( > BundleLoader.java:336) > at org.eclipse.osgi.internal.loader.BundleLoader.findClass( > BundleLoader.java:328) > at org.eclipse.osgi.internal.loader.ModuleClassLoader. > loadClass(ModuleClassLoader.java:160) > at java.lang.ClassLoader.loadClass(ClassLoader.java:357) > at org.apache.commons.configuration2.event.EventListenerList$ > EventListenerIterator.<init>(EventListener > List.java:308) > at org.apache.commons.configuration2.event.EventListenerList. > getEventListenerIterator(EventListenerList > .java:197) > at org.apache.commons.configuration2.event.EventListenerList.fire( > EventListenerList.java:158) > at org.apache.commons.configuration2.builder. > BasicConfigurationBuilder.fireBuilderEvent(BasicConfigurat > ionBuilder.java:636) > at org.apache.commons.configuration2.builder. > BasicConfigurationBuilder.getConfiguration(BasicConfigurat > ionBuilder.java:273) > at org.openmole.core.workspace.ConfigurationFile$$anonfun$ > org$openmole$core$workspace$ConfigurationFile > $$config$1.apply(Configuration.scala:65) > at org.openmole.core.workspace.ConfigurationFile$$anonfun$ > org$openmole$core$workspace$ConfigurationFile > $$config$1.apply(Configuration.scala:65) > at org.openmole.tool.thread.package$. > withThreadClassLoader(package.scala:66) > at org.openmole.core.workspace.ConfigurationF at > org.openmole.core.workspace.ConfigurationFile$$anonfun$ > value$1.apply(Configuration.scala:68) > at org.openmole.core.workspace.ConfigurationFile$$anonfun$ > value$1.apply(Configuration.scala:68) > at org.openmole.tool.lock.package$ReadWriteLockDecorator.read( > package.scala:48) > at org.openmole.core.workspace.ConfigurationFile.value( > Configuration.scala:67) > at org.openmole.core.workspace.Workspace.preferenceOption( > Workspace.scala:142) > at org.openmole.core.workspace.Workspace.preference( > Workspace.scala:150) > at org.openmole.core.workflow.execution.Environment$$ > anonfun$org$openmole$core$workflow$execution$Envir > onment$$_errors$1.apply$mcI$sp(Environment.scala:57) > at org.openmole.tool.collection.SlidingList.put(SlidingList. > scala:28) > at org.openmole.core.workflow.execution.Environment$class. > error(Environment.scala:58) > at org.openmole.plugin.environment.egi.DIRACEnvironment.error( > DIRACEnvironment.scala:83) > at org.openmole.plugin.environment.batch.refresh. > JobManager.$bang(JobManager.scala:133) > at org.openmole.plugin.environment.batch.refresh. > UploadActor.receive(UploadActor.scala:61) > at org.openmole.plugin.environment.batch.refresh. > JobManager$DispatcherActor$.receive(JobManager.scala:8 > 2) > at org.openmole.plugin.environment.batch.refresh. > JobManager$$anonfun$1$$anon$1.run(JobManager.scala:64) > Caused by: java.io.FileNotFoundException: /home/reyman/.openmole/.tmp/ > 1480105414_12098/org.eclipse.osgi/90/0/bu > ndleFile (Trop de fichiers ouverts) > at java.util.zip.ZipFile.open(Native Method) > at java.util.zip.ZipFile.<init>(ZipFile.java:219) > at java.util.zip.ZipFile.<init>(ZipFile.java:149) > at java.util.zip.ZipFile.<init>(ZipFile.java:163) > at org.eclipse.osgi.framework.util.SecureAction.getZipFile( > SecureAction.java:288) > ... 37 more > ile.org$openmole$core$workspace$ConfigurationFile$$config( > Configuration.scala:65) > > > 2016-11-25 13:31 GMT+01:00 Jonathan Passerat-Palmbach < > [email protected]>: > >> (moleTask on env) will do :) >> >> Just an operator priority issue ;) >> >> J. >> >> >> On 25 November 2016 12:21:34 GMT+00:00, sebastien rey coyrehourcq < >> [email protected]> wrote: >>> >>> HI Jo, >>> i tried, without success :-/ >>> >>> val moleTask = MoleTask(templateTask -- scriptTask) >>> exploration -< moleTask on env >>> >>> return >>> >>> org.openmole.core.console.ScalaREPL$CompilationError: (line 87) value >>> on is not a member of org.openmole.core.workflow.puzzle.Puzzle >>> exploration -< moleTask on env >>> >>> --- >>> Sébastien Rey Coyrehourcq >>> Research Engineer, BAP E, UMR IDEES >>> Sent from Nylas N1 <https://nylas.com/n1?ref=n1>, the extensible, open >>> source mail client. >>> >>> On nov. 25 2016, at 1:10 pm, Jonathan Passerat-Palmbach < >>> [email protected]> wrote: >>> >>>> Hey Seb, >>>> >>>> Try to wrap your two consecutive tasks in a MoleTask to apply the same >>>> env setting to both of them. >>>> >>>> http://www.openmole.org/current/Documentation_Language_Tasks_Mole.html >>>> >>>> Cheers >>>> J. >>>> >>>> On 25 November 2016 11:58:40 GMT+00:00, sebastien rey coyrehourcq < >>>> [email protected]> wrote: >>>> >>>> Hi guys, >>>> >>>> With env = LocalEnvironment(...) >>>> >>>> One little question about env position in final workflow, >>>> i need to run two task on grid node, so i position my env like that : >>>> >>>> val exploration = >>>> ExplorationTask( ...) >>>> >>>> val templateTask = >>>> TemplateFileTask(workDirectory / "parameters.xml", fileoutput) set >>>> ( .... ) >>>> >>>> val scriptTask = >>>> SystemExecTask("bash ./emergence2/script.sh ${fileoutput}") set ( ...) >>>> >>>> val copyFolder = CopyFileHook(folder, workDirectory / >>>> "results/${seeds(0)}_${tremble}_outputs") >>>> >>>> >>>> *exploration -< (templateTask -- scriptTask) on env hook copyFolder* >>>> >>>> I try other positions in the wf , but i have always a puzzle error : >>>> >>>> org.openmole.core.console.ScalaREPL$CompilationError: (line 85) value >>>> on is not a member of org.openmole.core.workflow.puzzle.Puzzle >>>> exploration -< templateTask on env -- scriptTask hook copyFolder >>>> // -- scriptTask2 hook ToStringHook() >>>> ^ >>>> >>>> Any idea ? >>>> >>>> --- >>>> Sébastien Rey Coyrehourcq >>>> Research Engineer, BAP E, UMR IDEES >>>> Sent from Nylas N1 <https://nylas.com/n1?ref=n1>, the extensible, open >>>> source mail client. >>>> >>>> ------------------------------ >>>> >>>> OpenMOLE-users mailing list >>>> [email protected] >>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >>>> >>>> >>>> -- >>>> Jonathan Passerat-Palmbach, PhD >>>> Research Associate >>>> Department of Computing >>>> Imperial College London >>>> >>>> South Kensington Campus >>>> Huxley Building - room 344 >>>> 180 Queen's Gate >>>> London SW7 2AZ >>> >>> ------------------------------ >>> >>> OpenMOLE-users mailing list >>> [email protected] >>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >>> >>> >> -- >> Jonathan Passerat-Palmbach, PhD >> Research Associate >> Department of Computing >> Imperial College London >> >> South Kensington Campus >> Huxley Building - room 344 >> 180 Queen's Gate >> London SW7 2AZ >> >> _______________________________________________ >> OpenMOLE-users mailing list >> [email protected] >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> > > > -- > <http://stackoverflow.com/users/385881/reyman64> > -- <http://stackoverflow.com/users/385881/reyman64>
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