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Why is java using 1000% of my CPU when running a single-threaded tool in gatk-protected.jar?

LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

I am running a tool that definitely only uses one core. However, when I look at top I see that I am using a large portion of the available cores on the machine.

Best Answer


  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭
    Accepted Answer

    You may need to limit the maximum number of garbage collection threads being used by Java.

    For example:
    java -XX:ConcGCThreads=1 -jar gatk-protected.jar .......

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