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Thread: Java heap space

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    Default Java heap space

    While i running Lucene search library,i am facing a problem
    Java heap space error.
    what is the reason behind this

  2. #2
    Petr's Avatar
    Petr is offline Senior Member
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    Hi. Can you show all stack trace ?
    Usually If you have Error problems it relate with performance java. I guess you have OutOfMemoryError. If it is so you need improve memory for java. You can it for help key Xmx or your app has leak memory.
    Last edited by Petr; 05-02-2011 at 11:26 AM.
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    Default Java heap space

    hi ,


    90168157 [main] ERROR cidms.pathway.index.IndexDTO - getAll -> java.lang.OutOfMemoryError: Java heap space
    90168969 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneIndex - document -> Java heap space
    90168969 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19494) getProteinGeneDetails -> CSN5_HUMAN
    90194422 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90198516 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19493) getProteinGeneDetails -> CREB1_HUMAN
    90229469 [main] ERROR cidms.pathway.index.IndexDTO - getAll -> java.lang.OutOfMemoryError: Java heap space
    90229485 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19492) getProteinGeneDetails -> CAH9_HUMAN
    90253407 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90256735 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19491) getProteinGeneDetails -> CXCR4_HUMAN
    90287063 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90291016 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19490) getProteinGeneDetails -> GTR1_HUMAN
    90315563 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90319266 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19489) getProteinGeneDetails -> EGLN3_HUMAN
    90348610 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90351953 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19488) getProteinGeneDetails -> ITB2_HUMAN
    90377813 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90382344 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19487) getProteinGeneDetails -> NOS2_HUMAN
    90408313 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90412250 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19486) getProteinGeneDetails -> NCOA1_HUMAN
    90442375 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90447266 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19485) getProteinGeneDetails -> EPO_HUMAN
    90472032 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90475766 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19484) getProteinGeneDetails -> LEP_HUMAN
    90506125 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - setInteractionDetails -> Java heap space
    90509766 [main] INFO cidms.pathway.index.proteingene.ProteinGeneDBA - (19483) getProteinGeneDetails -> MDR1_HUMAN
    90539532 [main] ERROR cidms.pathway.index.proteingene.ProteinGeneDBA - getPathwayDetails -> Java heap space
    90581188 [main] DEBUG cidms.pathway.index.IndexMain - Index Main Start -> Sat Apr 30 12:02:31 KST 2011
    90581188 [main] DEBUG cidms.pathway.index.IndexMain - Index Main End -> Sun May 01 13:12:12 KST 2011
    90581188 [main] DEBUG cidms.pathway.index.IndexMain - Index Time -> 1509 minutes

  4. #4
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    Can you show code from IndexDTO class?
    yes You need add memory for Java.
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  5. #5
    doWhile is offline Moderator
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    As Petr mentioned, add more memory using the -Xmx parameter (for example, when running the app add the -Xmx512m to the command line parameters to increase the maximum memory to 512mb). It looks like you are reading genome/proteome data, which is a lot of information and typically requires more memory than the default maximum heap memory java provides.

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