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  • Java problem when using BBmap

    Hi guys,

    I am working on a cluster that was changed to CentOS 7.3.1611 and SLURM scheduler recently. Since the change I cannot use any of the BBmap tools any longer, they all quit with a java error.

    For example:
    bbduk.sh -Xmx400m in=test.fq out=out.fq ftl=10

    results in:
    Error occurred during initialization of VM
    Could not reserve enough space for 819200KB object heap
    srun: error: a0150: task 0: Exited with exit code 1
    srun: Terminating job step 3196181.0

    I have Java 1.8.0_121 installed. Using the -Xms flag did not solve the problem either.

    Any ideas how to tackle the problem?
    Last edited by Lukas Hellmann; 10-23-2017, 05:10 AM.

  • #2
    Are you assigning memory e.g. "--mem=4g" (or the appropriate amount) in your SLURM command?

    I regularly use bbmap with SLURM and have not had any issues.

    Comment


    • #3
      Yes, I assign memory. I even tried to request huge excess memory to fulfill java requirements, but that did not help. I don't think job submission is the problem, as I have no issues with any other software.

      The OS was changed in addition. I suppose this causes the problems.

      Comment


      • #4
        I also use CentOS so that should not be a problem. Have you tried to talk with your sys admins? Are you able to run the jobs directly outside SLURM?

        Comment


        • #5
          java version "1.8.0_121"
          Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
          Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

          Comment

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