java.io.IOException: java.io.IOException: Cannot allocate memory|

Coderanch | Arul Jose | 9 years ago
  1. 0

    cannot allocate memory

    Coderanch | 9 years ago | Arul Jose
    java.io.IOException: java.io.IOException: Cannot allocate memory|
  2. 0

    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)

    JIRA | 8 years ago | Jim Procter
    java.io.IOException: java.io.IOException: Too many open files
  3. 0

    Loss of functionality due to too many open files errors - Atlassian Documentation

    atlassian.com | 7 months ago
    java.io.IOException: java.io.IOException: Too many open files
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    Cannot allocate memory exception&nbsp; - AMD64

    Oracle Community | 9 years ago | 843798
    java.io.IOException: java.io.IOException: Cannot allocate memory
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    Executing Unix Command Through Java

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    java.io.IOException: java.io.IOException: Cannot allocate memory

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Root Cause Analysis

  1. java.io.IOException

    java.io.IOException: Cannot allocate memory|

    at java.lang.UNIXProcess.<init>()
  2. Java RT
    Runtime.exec
    1. java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
    2. java.lang.ProcessImpl.start(ProcessImpl.java:65)
    3. java.lang.ProcessBuilder.start(ProcessBuilder.java:451)
    4. java.lang.Runtime.exec(Runtime.java:591)
    5. java.lang.Runtime.exec(Runtime.java:429)
    6. java.lang.Runtime.exec(Runtime.java:326)
    6 frames
  3. export
    ImageExportScheduler.executeTask
    1. export.StudioRobot.runRobot(Unknown Source)
    2. export.ImageExportScheduler.executeTask(Unknown Source)
    2 frames
  4. taskengine.internal
    SchedulerBean.executeTask
    1. taskengine.internal.SchedulerBean.executeTask(SchedulerBean.java:417)
    1 frame
  5. Java RT
    Method.invoke
    1. sun.reflect.GeneratedMethodAccessor56.invoke(Unknown Source)
    2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    3. java.lang.reflect.Method.invoke(Method.java:585)
    3 frames
  6. mfw.bean
    BeanProxy.invoke
    1. mfw.bean.BeanProxy.invoke(BeanProxy.java:119)
    1 frame
  7. Unknown
    $Proxy3.executeTask
    1. $Proxy3.executeTask(Unknown Source)
    1 frame
  8. taskengine.internal
    ScheduleExecutor.run
    1. taskengine.internal.ScheduleExecutor.executeNextTask(ScheduleExecutor.java:115)
    2. taskengine.internal.ScheduleExecutor.run(ScheduleExecutor.java:41)
    2 frames
  9. Java RT
    Thread.run
    1. java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    3. java.lang.Thread.run(Thread.java:595)
    3 frames