Hi Murat, it is due to a quota of number of process on the machine. OpenMOLE uses many threads to refresh jobs. You can lower this number in the preference file (~/.openmole/machinename/preferences). The property is called: BatchEnvironment.JobManagementThreads.
Romain Le 05/11/2015 04:46, Murat Yildizoglu a écrit : > Hi Romain, > > It was a stupid error, a comma missing just before the wallTime, now > solved. > I have also installed the version 5.9 on the front-end of the cluster. > > But I get the following problems when I try to run my script : > > (The log file indicated at the last line does not exist in that folder > (the folder itself does not exists in fact) > > / _ \ _ __ ___ _ __ | \/ |/ _ \| | | ____| | ___| > | | | | '_ \ / _ \ '_ \| |\/| | | | | | | _| |___ \ > | |_| | |_) | __/ | | | | | | |_| | |___| |___ ___) | > \___/| .__/ \___|_| |_|_| |_|\___/|_____|_____| |____/ > |_| > (Type :q to quit) > warning: there were two deprecation warnings; re-run with -deprecation > for details > warning: there were 58 feature warnings; re-run with -feature for details > !SESSION 2015-11-05 10:21:21.123 > ----------------------------------------------- > eclipse.buildId=unknown > java.version=1.7.0_03 > java.vendor=Oracle Corporation > BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=fr_FR > Framework arguments: -cp /home/yildi/openmole/openmole-plugins -gp > /home/yildi/openmole/openmole-plugins-gui -s ./vdmy5avakas.oms -pw lokum > Command-line arguments: -consoleLog -cp > /home/yildi/openmole/openmole-plugins -gp > /home/yildi/openmole/openmole-plugins-gui -s ./vdmy5avakas.oms -pw lokum > > !ENTRY org.eclipse.osgi 4 0 2015-11-05 10:21:46.518 > !MESSAGE Application error > !STACK 1 > java.lang.OutOfMemoryError: unable to create new native thread > at java.lang.Thread.start0(Native Method) > at java.lang.Thread.start(Thread.java:691) > at > org.openmole.core.batch.refresh.JobManager$$anonfun$1.apply(JobManager.scala:68) > at > org.openmole.core.batch.refresh.JobManager$$anonfun$1.apply(JobManager.scala:61) > at scala.collection.immutable.Range.foreach(Range.scala:166) > at > org.openmole.core.batch.refresh.JobManager.<init>(JobManager.scala:61) > at > org.openmole.core.batch.environment.BatchEnvironment$.jobManager$lzycompute(BatchEnvironment.scala:133) > at > org.openmole.core.batch.environment.BatchEnvironment$.jobManager(BatchEnvironment.scala:133) > at > org.openmole.core.batch.environment.BatchEnvironment$class.submit(BatchEnvironment.scala:192) > at > org.openmole.plugin.environment.pbs.PBSEnvironment.submit(PBSEnvironment.scala:69) > at org.openmole.core.workflow.mole.MoleExecution.org > <http://org.openmole.core.workflow.mole.MoleExecution.org>$openmole$core$workflow$mole$MoleExecution$$submit(MoleExecution.scala:150) > at > org.openmole.core.workflow.mole.MoleExecution$$anonfun$group$2.apply(MoleExecution.scala:145) > at > org.openmole.core.workflow.mole.MoleExecution$$anonfun$group$2.apply(MoleExecution.scala:145) > at scala.Option.map(Option.scala:146) > at > org.openmole.core.workflow.mole.MoleExecution.group(MoleExecution.scala:145) > at > org.openmole.core.workflow.mole.SubMoleExecution.submit(SubMoleExecution.scala:231) > at > org.openmole.core.workflow.transition.ITransition$class.submitNextJobsIfReady(ITransition.scala:115) > at > org.openmole.core.workflow.transition.ExplorationTransition.submitNextJobsIfReady(ExplorationTransition.scala:31) > at > org.openmole.core.workflow.transition.ExplorationTransition$$anonfun$submitIn$1.apply(ExplorationTransition.scala:65) > at > org.openmole.core.workflow.transition.ExplorationTransition$$anonfun$submitIn$1.apply(ExplorationTransition.scala:49) > at scala.collection.immutable.List.foreach(List.scala:381) > at > org.openmole.core.workflow.transition.ExplorationTransition.submitIn(ExplorationTransition.scala:49) > at > org.openmole.core.workflow.transition.ExplorationTransition$$anonfun$perform$1.apply$mcV$sp(ExplorationTransition.scala:37) > at > org.openmole.core.workflow.transition.ExplorationTransition$$anonfun$perform$1.apply(ExplorationTransition.scala:37) > at > org.openmole.core.workflow.transition.ExplorationTransition$$anonfun$perform$1.apply(ExplorationTransition.scala:37) > at > org.openmole.tool.lock.package$LockDecorator.apply(package.scala:28) > at > org.openmole.core.workflow.transition.ExplorationTransition.perform(ExplorationTransition.scala:37) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$jobFinished$1$$anonfun$apply$mcV$sp$3.apply(SubMoleExecution.scala:149) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$jobFinished$1$$anonfun$apply$mcV$sp$3.apply(SubMoleExecution.scala:149) > at scala.collection.immutable.List.foreach(List.scala:381) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$jobFinished$1.apply$mcV$sp(SubMoleExecution.scala:149) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$jobFinished$1.apply(SubMoleExecution.scala:149) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$jobFinished$1.apply(SubMoleExecution.scala:149) > at > org.openmole.tool.lock.package$LockDecorator.apply(package.scala:28) > at > org.openmole.core.workflow.mole.SubMoleExecution.jobFinished(SubMoleExecution.scala:148) > at > org.openmole.core.workflow.mole.SubMoleExecution.finalState(SubMoleExecution.scala:266) > at org.openmole.core.workflow.mole.SubMoleExecution.org > <http://org.openmole.core.workflow.mole.SubMoleExecution.org>$openmole$core$workflow$mole$SubMoleExecution$$stateChanged$2(SubMoleExecution.scala:225) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$11.apply(SubMoleExecution.scala:228) > at > org.openmole.core.workflow.mole.SubMoleExecution$$anonfun$11.apply(SubMoleExecution.scala:228) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(LocalExecutor.scala:80) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(LocalExecutor.scala:78) > nov. 05, 2015 10:21:46 AM org.openmole.core.updater.UpdaterTask run > Avertissement: null > java.lang.OutOfMemoryError: unable to create new native thread > at java.lang.Thread.start0(Native Method) > at java.lang.Thread.start(Thread.java:691) > at > java.util.concurrent.ThreadPoolExecutor.addWorker(ThreadPoolExecutor.java:943) > at > java.util.concurrent.ThreadPoolExecutor.prestartCoreThread(ThreadPoolExecutor.java:1544) > at > java.util.concurrent.ScheduledThreadPoolExecutor.delayedExecute(ScheduledThreadPoolExecutor.java:333) > at > java.util.concurrent.ScheduledThreadPoolExecutor.schedule(ScheduledThreadPoolExecutor.java:530) > at org.openmole.core.updater.Updater$.delay(Updater.scala:49) > at org.openmole.core.updater.UpdaterTask.run(UpdaterTask.scala:29) > at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) > at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) > at java.util.concurrent.FutureTask.run(FutureTask.java:166) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) > at java.lang.Thread.run(Thread.java:722) > > at > org.openmole.core.workflow.job.MoleJob.signalChanged(MoleJob.scala:90) > at org.openmole.core.workflow.job.MoleJob.state_$eq(MoleJob.scala:94) > at org.openmole.core.workflow.job.MoleJob.perform(MoleJob.scala:101) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1$$anonfun$apply$1.apply(LocalExecutor.scala:83) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1$$anonfun$apply$1.apply(LocalExecutor.scala:64) > at scala.collection.immutable.List.foreach(List.scala:381) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1.apply(LocalExecutor.scala:64) > at > org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1.apply(LocalExecutor.scala:61) > at > org.openmole.core.workflow.execution.local.LocalExecutor.withRedirectedOutput(LocalExecutor.scala:126) > at > org.openmole.core.workflow.execution.local.LocalExecutor.run(LocalExecutor.scala:61) > at java.lang.Thread.run(Thread.java:722) > An error has occurred. See the log file > */home/yildi/.openmole/.tmp/1446715280_1251/1446715281608.log.* > > 2015-11-05 5:01 GMT+01:00 Romain Reuillon <romain.reuil...@iscpif.fr > <mailto:romain.reuil...@iscpif.fr>>: > > Could you provide the corresponding oms ? > > > Le 05/11/2015 00:40, Murat Yildizoglu a écrit : >> Hi Romain, >> >> When I do this, I get another error in the console (while this >> instruction seems to works without any problem when I launch this >> model from the web interface: >> >> ___ __ __ ___ _ _____ ____ >> / _ \ _ __ ___ _ __ | \/ |/ _ \| | | ____| | ___| >> | | | | '_ \ / _ \ '_ \| |\/| | | | | | | _| |___ \ >> | |_| | |_) | __/ | | | | | | |_| | |___| |___ ___) | >> \___/| .__/ \___|_| |_|_| |_|\___/|_____|_____| |____/ >> |_| >> (Type :q to quit) >> <console>:248: error: value wallTime is not a member of String >> possible cause: maybe a semicolon is missing before `value wallTime'? >> wallTime=1 hours, >> ^ >> <console>:379: error: value wallTime is not a member of String >> possible cause: maybe a semicolon is missing before `value wallTime'? >> wallTime=1 hours, >> ^ >> org.openmole.core.exception.UserBadDataError: Compilation error: >> value wallTime is not a member of String >> possible cause: maybe a semicolon is missing before `value wallTime'? >> wallTime=1 hours, >> ^ >> on line 248 >> Compilation error: >> value wallTime is not a member of String >> possible cause: maybe a semicolon is missing before `value wallTime'? >> wallTime=1 hours, >> ^ >> on line 379 >> >> at >> >> org.openmole.core.console.ScalaREPL.messageToException(ScalaREPL.scala:74) >> at >> org.openmole.core.console.ScalaREPL.compile(ScalaREPL.scala:92) >> at org.openmole.console.Project.compile(Project.scala:64) >> at org.openmole.console.Project.compile(Project.scala:58) >> at org.openmole.console.Console.run(Console.scala:159) >> at >> org.openmole.ui.Application$$anonfun$start$1.apply(Application.scala:184) >> at >> org.openmole.ui.Application$$anonfun$start$1.apply(Application.scala:60) >> at >> >> org.openmole.core.replication.DBServerRunning$.useDB(DBServerRunning.scala:42) >> at org.openmole.ui.Application.start(Application.scala:60) >> at org.openmole.ui.Application.start(Application.scala:47) >> at >> >> org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) >> at >> >> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) >> at >> >> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) >> at >> >> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:353) >> at >> >> org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:180) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) >> at >> >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> at java.lang.reflect.Method.invoke(Method.java:601) >> at >> org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:629) >> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:584) >> at org.eclipse.equinox.launcher.Main.run(Main.java:1438) >> at org.eclipse.equinox.launcher.Main.main(Main.java:1414) >> >> 2015-11-04 18:59 GMT+01:00 Romain Reuillon >> <romain.reuil...@iscpif.fr <mailto:romain.reuil...@iscpif.fr>>: >> >> Hi Murat, >> >> if you rename your file with no dash in it, it will work, >> >> I keep that in mind to make it more robust at some point.... >> >> Romain >> >> >> >> Le 04/11/2015 16:38, Murat Yildizoglu a écrit : >>> Hi, >>> >>> I have been able to make the experiment index working thanks >>> to your indications. >>> I must say that the Samples page is not very helpful on this >>> and I could not make it without your help. Thanks a lot! >>> >>> Now that everything works on my laptop, and on the cluster >>> from my laptop, I would like to launch my simulations >>> directly from the front-end of the cluster, while being able >>> to disconnect from it and let it run. >>> >>> Of course what I need is the headless version of the script. >>> Unfortunately, when I run the command given on the web page >>> >>> |./openmole -s /path/to/your/mole/script -pw password >>> >>> | >>> |using my path, my script and my password, OM Console opens >>> and complains that the namr of my script is not a command >>> >>> (Type :q to quit) >>> <console>:2: error: ';' expected but identifier found. >>> class vdmy4-avakasClass { >>> ^ >>> <console>:213: error: illegal start of simple expression >>> ) >>> ^ >>> <console>:261: error: ')' expected but '}' found. >>> } >>> ^ >>> org.openmole.core.exception.UserBadDataError: Compilation error: >>> ';' expected but identifier found. >>> class vdmy4-avakasClass { >>> >>> >>> | >>> |Is this -s switch correct? Why it is launching the console >>> instead of running my script? >>> | >>> | >>> | >>> >>> -- >>> Prof. Murat Yildizoglu >>> >>> Note: Please use the following address as such >>> >>> UNIVERSITE DE BORDEAUX >>> GREThA (UMR CNRS 5113) >>> MURAT YILDIZOGLU >>> 16 AVENUE LEON DUGUIT >>> CS 50057 >>> 33608 PESSAC CEDEX >>> FRANCE >>> >>> Bureau : E-331 >>> >>> mail: murat.yildizoglu at u-bordeaux.fr <http://u-bordeaux.fr> >>> >>> web: www.yildizoglu.fr <http://www.yildizoglu.fr> >>> >>> >>> _______________________________________________ >>> OpenMOLE-users mailing list >>> OpenMOLE-users@iscpif.fr <mailto:OpenMOLE-users@iscpif.fr> >>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> >> _______________________________________________ >> OpenMOLE-users mailing list >> OpenMOLE-users@iscpif.fr <mailto:OpenMOLE-users@iscpif.fr> >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> >> >> >> -- >> Prof. Murat Yildizoglu >> >> Note: Please use the following address as such >> >> UNIVERSITE DE BORDEAUX >> GREThA (UMR CNRS 5113) >> MURAT YILDIZOGLU >> 16 AVENUE LEON DUGUIT >> CS 50057 >> 33608 PESSAC CEDEX >> FRANCE >> >> Bureau : E-331 >> >> mail: murat.yildizoglu at u-bordeaux.fr <http://u-bordeaux.fr> >> >> web: www.yildizoglu.fr <http://www.yildizoglu.fr> >> >> >> _______________________________________________ >> OpenMOLE-users mailing list >> OpenMOLE-users@iscpif.fr <mailto:OpenMOLE-users@iscpif.fr> >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users > > > _______________________________________________ > OpenMOLE-users mailing list > OpenMOLE-users@iscpif.fr <mailto:OpenMOLE-users@iscpif.fr> > http://fedex.iscpif.fr/mailman/listinfo/openmole-users > > > > > -- > Prof. Murat Yildizoglu > > Note: Please use the following address as such > > UNIVERSITE DE BORDEAUX > GREThA (UMR CNRS 5113) > MURAT YILDIZOGLU > 16 AVENUE LEON DUGUIT > CS 50057 > 33608 PESSAC CEDEX > FRANCE > > Bureau : E-331 > > mail: murat.yildizoglu at u-bordeaux.fr <http://u-bordeaux.fr> > > web: www.yildizoglu.fr <http://www.yildizoglu.fr> > > > _______________________________________________ > OpenMOLE-users mailing list > OpenMOLE-users@iscpif.fr > http://fedex.iscpif.fr/mailman/listinfo/openmole-users
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