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]> 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 > > _______________________________________________ > 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
