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]> 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] > http://fedex.iscpif.fr/mailman/listinfo/openmole-users
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