Sounds like a good candidate for a new FAQ entry ;)
On 26 November 2016 00:44:32 CET, Romain Reuillon <[email protected]>
wrote:
>You can generally increase the number of openfiles using: ulimit -n
>10240 (you should execute it in the current bash before running
>openmole)
>
>Le 26/11/2016 à 00:41, Romain Reuillon a écrit :
>> It mean that you have an ulimit set tow low. Can you send the result
>> of ulimit -a ?
>>
>> Le 25/11/2016 à 21:37, reyman a écrit :
>>> 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]
>>> <mailto:[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$1.run(JobManager.scala:64)
>>> Caused by: java.io.FileNotFoundException:
>>>
>/home/reyman/.openmole/.tmp/1480105414_12098/org.eclipse.osgi/90/0/bu
>>> ndleFile (Trop de fichiers ouverts)
>>> at java.util.zip.ZipFile.open(Native Method)
>>> at java.util.zip.ZipFile.<init>(ZipFile.java:219)
>>> at java.util.zip.ZipFile.<init>(ZipFile.java:149)
>>> at java.util.zip.ZipFile.<init>(ZipFile.java:163)
>>> at
>>>
>org.eclipse.osgi.framework.util.SecureAction.getZipFile(SecureAction.java:288)
>>> ... 37 more
>>> ile.org
>>>
><http://ile.org>$openmole$core$workspace$ConfigurationFile$$config(
>>> Configuration.scala:65)
>>>
>>>
>>> 2016-11-25 13:31 GMT+01:00 Jonathan Passerat-Palmbach
>>> <[email protected]
>>> <mailto:[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] <mailto:[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]
>>> <mailto:[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
>>>
><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]
>>> <mailto:[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]
>>> <mailto:[email protected]>
>>>
>http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>>
><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]
><mailto:[email protected]>
>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>> <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]
>>> <mailto:[email protected]>
>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>> <http://fedex.iscpif.fr/mailman/listinfo/openmole-users>
>>>
>>> --
>>> <http://stackoverflow.com/users/385881/reyman64>
>>>
>>> --
>>> <http://stackoverflow.com/users/385881/reyman64>
>>>
>>> _______________________________________________
>>> OpenMOLE-users mailing list
>>> [email protected]
>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>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
_______________________________________________
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