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BaseRecalibrator doesn't respect -Xmx and -Xms settings
GATK version: version 2.1-12-g2d7797a
I'm using open grid engine via "starcluster", and have cluster nodes with 21G of ram. I have h_vmem as a requestable resource.
My qsub command requests "-l h_vmem=7G" and the java command is "java -Xms1G -Xmx5G -jar GenomeAnalysisTKLite.jar -T BaseRecalibrator ..."
the linux kernel/open grid engine kills the job:
main|node003|W|job 2271 exceeds job hard limit "h_vmem" of queue "[email protected]" (11716157440.00000 > limit:7516192768.00000) - sending SIGKILL
I've been reading about what I might be not specifying when trying to constrain the process, and perhaps I need to also add -XX:MaxPermSize to something specific ?