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CPU usage

erikterikt Member

Happy Friday!

I am running GATK on a shared LSF cluster but have unintentionally run afoul of the admins due to resource use. I am running the GATK commands with 'java -Xmx4g -jar $GATK' and am not using -nt or -nct, but CPU usage is exceeding the resources requested which are 1 vCore and 6G memory. I am now running the same commands on our lab server and do indeed see that CPU usage reaches as high as 800% at times. Is there a way to limit the CPU resources claimed by GATK tools, or alternatively a way to anticipate its actual needs so that I can request an appropriate number of CPUs?

Much thanks,
Erik

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