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I have two queues in SGE for different purposes. Each of them has a limit in slots. What I want is to have only a certain number of jobs submitted to a queue waiting even when the other queue is idle. However, what I found is the additional jobs were assigned to the second queue. How should I change the configuration?

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I'm not sure I understand your question. You want jobs to wait for a queue to become available, up until you reach a certain number of jobs, and only then utilize the other queue? – Kamil Kisiel Nov 17 '11 at 19:31
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You need to specify the queue name when submitting:

qsub -l qname=<queue name> ...

Then the other queue will not be used.

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