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  • GitHub comment 500#111537428
    via GitHub by activeeon-bot
    ,
  • A server 'event' appeared to occur on Monday 13th October 2008. Excerpts from the vamsas.log file for this event are in additional information. lsof wasn't used on the process to verify the problem - the service was simply restarted. This took some time, due to a particularly high load on the box (around 15). It is unclear if this event was due to side effects from other services (e.g. the cruisecontrol service under the ws-dev1 user which was started around the same time the problem was observed). ****** ADDITIONAL INFORMATION ****** ERROR 2008-10-13 14:09:11,260 TP-Processor38 vamsas.secstrpred.jpred3 Error whil st handling /fc_gpfs/gjb_lab/www-jpred/results/jp_YtSdQW2 java.io.FileNotFoundException: /fc_gpfs/gjb_lab/www-jpred/results/jp_YtSdQW2/LOG (Too many open files) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:106) at java.io.FileReader.<init>(FileReader.java:55) at vamsas.WebService.fileMatches(WebService.java:307) at vamsas.secstrpred.jpred3.getresult(jpred3.java:379) at sun.reflect.GeneratedMethodAccessor116.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces sorImpl.java:25) .. WARN 2008-10-13 14:20:26,157 TP-Processor34 vamsas.SungridJob Exception for qsub -N clustalw37653 -l h_cpu=01:00:00,h_vmem=1024M -P webservices -e /fc_gpfs/g jb_lab/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37653/STDERR -o /fc_gpfs/gjb_la b/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37653/STDOUT java.io.IOException: java.io.IOException: Too many open files at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) .. WARN 2008-10-13 14:28:02,625 TP-Processor33 vamsas.SungridJob Exception for qsub -N clustalw37658 -l h_cpu=01:00:00,h_vmem=1024M -P webservices -e /fc_gpfs/g jb_lab/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37658/STDERR -o /fc_gpfs/gjb_la b/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37658/STDOUT java.io.IOException: java.io.IOException: Too many open files at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) .. WARN 2008-10-13 14:29:45,775 TP-Processor47 vamsas.SungridJob Exception for qsub -N clustalw37659 -l h_cpu=01:00:00,h_vmem=1024M -P webservices -e /fc_gpfs/g jb_lab/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37659/STDERR -o /fc_gpfs/gjb_la b/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/clustalw37659/STDOUT java.io.IOException: java.io.IOException: Too many open files at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) at vamsas.SungridJob.Submitjob(SungridJob.java:446) at vamsas.SungridJob.Submitjob(SungridJob.java:408) at vamsas.SungridJob.Submitjob(SungridJob.java:399) at vamsas.msa.ClustalWS.align(ClustalWS.java:142) WARN 2008-10-13 14:32:47,376 TP-Processor21 vamsas.SungridJob Exception for qsub -N muscle37660 -l h_cpu=01:00:00,h_vmem=1024M -P webservices -e /fc_gpfs/gjb _lab/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/muscle37660/STDERR -o /fc_gpfs/gjb_lab/ws -dev1/jobs/JalviewWS/MsaWS-Jobs/muscle37660/STDOUT java.io.IOException: java.io.IOException: Too many open files at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) at vamsas.SungridJob.Submitjob(SungridJob.java:446) at vamsas.SungridJob.Submitjob(SungridJob.java:408) at vamsas.SungridJob.Submitjob(SungridJob.java:399) at vamsas.msa.MuscleWS.align(MuscleWS.java:107) .. WARN 2008-10-13 14:33:59,944 TP-Processor18 vamsas.SungridJob Exception for qsub -N muscle37661 -l h_cpu=01:00:00,h_vmem=1024M -P webservices -e /fc_gpfs/gjb _lab/ws-dev1/jobs/JalviewWS/MsaWS-Jobs/muscle37661/STDERR -o /fc_gpfs/gjb_lab/ws -dev1/jobs/JalviewWS/MsaWS-Jobs/muscle37661/STDOUT java.io.IOException: java.io.IOException: Too many open files at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) at vamsas.SungridJob.Submitjob(SungridJob.java:446) at vamsas.SungridJob.Submitjob(SungridJob.java:408) at vamsas.SungridJob.Submitjob(SungridJob.java:399) at vamsas.msa.MuscleWS.align(MuscleWS.java:107)
    via by Jim Procter,
  • cannot allocate memory
    via by Arul Jose,
  • Executing Unix Command Through Java
    via by Aulia Yusuf,
  • Executing Unix command through Java
    via by 807607,
  • On Linux, if two variables path and PATH environment variables are set. Then builds on maven will fail with an error "env: not found" see stack trace below. Apparently PATH is ignored and path is used to launch maven. [webstickCore] $ /exec/products/jdk1.5.0_16/bin/java -cp /exec/products/tomcat_hudson/webapps/hudson/WEB-INF/lib/maven-agent-1.262.jar:/exec/products/maven/boot/classworlds-1.1.jar hudson.maven.agent.Main /exec/products/maven /exec/products/tomcat_hudson/webapps/hudson/WEB-INF/lib/remoting-1.262.jar /exec/products/tomcat_hudson/webapps/hudson/WEB-INF/lib/maven-interceptor-1.262.jar 39693 channel started Executing Maven: -B -B -f /data/hudson/jobs/webstickCore/workspace/webstickCore/pom.xml clean Error getting environment vars for profile activation: java.io.IOException: java.io.IOException: env: not found [WARNING] Failed to initialize environment variable resolver. Skipping environment substitution in settings. [WARNING] Failed to initialize environment variable resolver. Skipping environment substitution in settings. channel stopped ERROR: Failed to parse POMs hudson.util.IOException2 at hudson.maven.MavenBuilder.call(MavenBuilder.java:188) at hudson.maven.MavenModuleSetBuild$Builder.call(MavenModuleSetBuild.java:542) at hudson.maven.MavenModuleSetBuild$Builder.call(MavenModuleSetBuild.java:488) at hudson.remoting.UserRequest.perform(UserRequest.java:69) at hudson.remoting.UserRequest.perform(UserRequest.java:23) at hudson.remoting.Request$2.run(Request.java:213) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269) at java.util.concurrent.FutureTask.run(FutureTask.java:123) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675) at java.lang.Thread.run(Thread.java:595) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at hudson.maven.agent.Main.launch(Main.java:134) at hudson.maven.MavenBuilder.call(MavenBuilder.java:139) ... 11 more Caused by: java.io.IOException: java.io.IOException: env: not found at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) at hidden.org.codehaus.plexus.util.cli.CommandLineUtils.getSystemEnvVars(CommandLineUtils.java:250) at hidden.org.codehaus.plexus.util.cli.CommandLineUtils.getSystemEnvVars(CommandLineUtils.java:216) at org.apache.maven.project.interpolation.RegexBasedModelInterpolator.<init>(RegexBasedModelInterpolator.java:63) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:494) at java.lang.Class.newInstance0(Class.java:350) at java.lang.Class.newInstance(Class.java:303) at org.codehaus.plexus.component.factory.java.JavaComponentFactory.newInstance(JavaComponentFactory.java:44) at org.codehaus.plexus.DefaultPlexusContainer.createComponentInstance(DefaultPlexusContainer.java:1464) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:93) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:92) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:331) at org.codehaus.plexus.component.composition.FieldComponentComposer.assignRequirementToField(FieldComponentComposer.java:129) at org.codehaus.plexus.component.composition.FieldComponentComposer.assembleComponent(FieldComponentComposer.java:73) at org.codehaus.plexus.component.composition.DefaultComponentComposerManager.assembleComponent(DefaultComponentComposerManager.java:68) at org.codehaus.plexus.DefaultPlexusContainer.composeComponent(DefaultPlexusContainer.java:1486) at org.codehaus.plexus.personality.plexus.lifecycle.phase.CompositionPhase.execute(CompositionPhase.java:29) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:101) at org.codehaus.plexus.component.manager.AbstractComponentManager.startComponentLifecycle(AbstractComponentManager.java:105) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:95) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:92) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:331) at org.codehaus.plexus.component.composition.FieldComponentComposer.assignRequirementToField(FieldComponentComposer.java:129) at org.codehaus.plexus.component.composition.FieldComponentComposer.assembleComponent(FieldComponentComposer.java:73) at org.codehaus.plexus.component.composition.DefaultComponentComposerManager.assembleComponent(DefaultComponentComposerManager.java:68) at org.codehaus.plexus.DefaultPlexusContainer.composeComponent(DefaultPlexusContainer.java:1486) at org.codehaus.plexus.personality.plexus.lifecycle.phase.CompositionPhase.execute(CompositionPhase.java:29) at org.codehaus.plexus.lifecycle.AbstractLifecycleHandler.start(AbstractLifecycleHandler.java:101) at org.codehaus.plexus.component.manager.AbstractComponentManager.startComponentLifecycle(AbstractComponentManager.java:105) at org.codehaus.plexus.component.manager.AbstractComponentManager.createComponentInstance(AbstractComponentManager.java:95) at org.codehaus.plexus.component.manager.ClassicSingletonComponentManager.getComponent(ClassicSingletonComponentManager.java:92) at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:331) at org.codehaus.plexus.embed.Embedder.lookup(Embedder.java:78) at org.apache.maven.cli.MavenCli.createMavenInstance(MavenCli.java:479) at org.apache.maven.cli.MavenCli.main(MavenCli.java:262) ... 19 more finished: FAILURE
    via by vergnes,
  • Graylog2 won't start on Windows
    via GitHub by garethky
    ,
    • java.io.IOException: java.io.IOException: /opt/java/x86/bea/jrmc-3.0.3-1.5.0/jre/../bin/jstack: not found at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) at java.lang.ProcessImpl.start(ProcessImpl.java:65) at java.lang.ProcessBuilder.start(ProcessBuilder.java:451) at java.lang.Runtime.exec(Runtime.java:591) at java.lang.Runtime.exec(Runtime.java:429) at java.lang.Runtime.exec(Runtime.java:326) at functionalTests.FunctionalTest$2.run(FunctionalTest.java:191) at java.util.TimerThread.mainLoop(Timer.java:512) at java.util.TimerThread.run(Timer.java:462)

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