Ça sent plutot le pb de gama qui se comporte pas pareil sur grille et en local... est-ce que tu as des choses qui pourraient aider à diagnostiquer dans la sortie standard?
Le 26/11/2016 à 15:28, sebastien rey coyrehourcq a écrit : > Je switch en francais, plus facile à expliquer, car j'ai un problème > chelou encore. > > Sur la même expérience/wf j'obtient des outputs très différents entre > la grille et l'execution locale sur zebulon. Sur l'execution locale > les csv sont cohérents (j'ai bien le déroulement de l'expérience step > par step dans mon csv, et les valeurs varient bien en fct des > parametres), par contre les outputs qui me reviennent de grille, à > valeur de parametre équivalents, ne contiennent que les entetes et le > premier step de ma simulation. Ca peut arriver une fois du fait de la > condition darret, mais là tout les milliers de fichiers sont > semblables !! > > Je sais pas si c'est un probleme au niveau de la recopie des fichiers, > mais y a un soucis quelque part. > > --- > 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. 26 2016, at 12:17 pm, Romain Reuillon > <[email protected]> wrote: > > It seems like you can go up to 4096 without modifying anything on > ubuntu: ulimit -S -n 4096. I don't know how to go further up if > you find it, we'll add it to the FAQ. > > I didn't get the second question. > > > Le 26/11/2016 à 11:58, sebastien rey coyrehourcq a écrit : >> Thanks, >> Ubuntu refuse my try to modify this file limit : ulimit: value >> exceeds hard limit >> >> I modify the etc/security/limits.conf and reboot, but >> ulimit continue to be limited, don't know why. >> >> Also, is there a way to better prevent "java heap space" problem >> for users (FAQ, or directly in the software) >> >> --- >> 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. 26 2016, at 11:39 am, Romain Reuillon >> <[email protected]> <mailto:[email protected]> >> wrote: >> >> Totally agree. I'll do that prior to 6.1. >> >> BTW: the default limit on zebulon has been increased to >> 10240, this should be okay. >> >> Le 26/11/2016 à 09:29, Jonathan Passerat-Palmbach a écrit : >>> Sounds like a good candidate for a new FAQ entry ;) >>> >>> On 26 November 2016 00:44:32 CET, Romain Reuillon >>> <[email protected]> >>> <mailto:[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] <mailto:[email protected]> >>>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >>>> >>> >>> ------------------------------------------------------------------------ >>> >>> OpenMOLE-users mailing list >>> [email protected] <mailto:[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] <mailto:[email protected]> >>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> _______________________________________________ >> OpenMOLE-users mailing list >> [email protected] <mailto:[email protected]> >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users > > _______________________________________________ > OpenMOLE-users mailing list > [email protected] > http://fedex.iscpif.fr/mailman/listinfo/openmole-users
signature.asc
Description: OpenPGP digital signature
_______________________________________________ OpenMOLE-users mailing list [email protected] http://fedex.iscpif.fr/mailman/listinfo/openmole-users
