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LSF job resource allocation with Queue

Greetings GATK Team,

I am working with Queue for the GATK and am having some difficulties getting the resource allocation aspect to work on our cluster using LSF. I have used the command line options -memLimit, -resMemLimit and -jobNative to allocate the memory needed for the jobs spurred by Queue. When looking at the jobs after their submission, they do not seem to have requested the resources I specified.

Likewise, I would like to specify how many cores to reserve for each job and assume I do that with -jobNative (-n 4,4, for instance). Again, the allocation doesn't seem to show up in the job description as being requested and watching the job indicates that Queue ignores it.

Can you help me to work through this?

thanks for the great toolkit,

Jason

Answers

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