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Old 10-23-2017, 05:52 AM   #1
Lukas Hellmann
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Location: Germany

Join Date: Jul 2015
Posts: 3
Default 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 at 06:10 AM.
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Old 10-23-2017, 05:55 AM   #2
GenoMax
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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.
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Old 10-23-2017, 06:10 AM   #3
Lukas Hellmann
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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.
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Old 10-23-2017, 06:21 AM   #4
GenoMax
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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?
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Old 10-23-2017, 06:23 AM   #5
Lukas Hellmann
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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)
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